Starting phenix.real_space_refine on Sun Dec 29 22:48:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rxg_24730/12_2024/7rxg_24730.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rxg_24730/12_2024/7rxg_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_24730/12_2024/7rxg_24730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rxg_24730/12_2024/7rxg_24730.map" model { file = "/net/cci-nas-00/data/ceres_data/7rxg_24730/12_2024/7rxg_24730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rxg_24730/12_2024/7rxg_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-5532/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: 7.90, per 1000 atoms: 0.69 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: 3.71 Conformation dependent library (CDL) restraints added in 1.5 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: 1.07 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: 3.73 Time building geometry restraints manager: 3.60 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: 3.710 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: 0.270 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 29.430 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.860 ------------------------------------------------------------------------------- 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= 0.504 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 *********************** 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 : 1.287 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: 1.7419 time to fit residues: 337.2570 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 : 1.143 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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= 0.166 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 *********************** 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 : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.7513 (mmtp) cc_final: 0.6976 (mttm) REVERT: B 69 LYS cc_start: 0.7497 (mtmm) cc_final: 0.7268 (mttm) REVERT: B 305 GLU cc_start: 0.7622 (tp30) cc_final: 0.7314 (tm-30) REVERT: B 601 GLU cc_start: 0.6399 (mm-30) cc_final: 0.5808 (mm-30) REVERT: B 606 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6153 (mtp85) REVERT: B 629 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7314 (ttm110) REVERT: B 707 MET cc_start: 0.7042 (mtp) cc_final: 0.6802 (mtp) REVERT: A 35 LYS cc_start: 0.7527 (mmtp) cc_final: 0.6993 (mttm) REVERT: A 42 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7040 (mm-30) REVERT: A 69 LYS cc_start: 0.7476 (mtmm) cc_final: 0.7257 (mttm) REVERT: A 305 GLU cc_start: 0.7641 (tp30) cc_final: 0.7336 (tm-30) REVERT: A 601 GLU cc_start: 0.6485 (mm-30) cc_final: 0.5854 (mm-30) REVERT: A 606 ARG cc_start: 0.7220 (OUTLIER) cc_final: 0.6114 (mtp85) REVERT: A 629 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7318 (ttm110) outliers start: 21 outliers final: 10 residues processed: 150 average time/residue: 1.6109 time to fit residues: 258.7074 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 : 1.499 ------------------------------------------------------------------------------- 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 65 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11490 Z= 0.237 Angle : 0.568 4.777 15482 Z= 0.307 Chirality : 0.042 0.177 1670 Planarity : 0.005 0.038 1902 Dihedral : 22.456 168.139 2034 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.59 % Allowed : 6.70 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1288 helix: 1.90 (0.17), residues: 890 sheet: 0.74 (0.72), residues: 44 loop : -1.32 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 227 HIS 0.010 0.002 HIS B 619 PHE 0.015 0.002 PHE B 419 TYR 0.016 0.002 TYR A 589 ARG 0.003 0.001 ARG B 647 *********************** 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 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.207 Fit side-chains REVERT: B 42 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7036 (mm-30) REVERT: B 69 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7433 (mttm) REVERT: B 102 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: B 145 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: B 305 GLU cc_start: 0.7551 (tp30) cc_final: 0.7257 (tm-30) REVERT: B 601 GLU cc_start: 0.6519 (mm-30) cc_final: 0.5832 (mm-30) REVERT: B 606 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6235 (mtp85) REVERT: B 629 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7306 (ttm110) REVERT: A 42 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6990 (mm-30) REVERT: A 102 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.6322 (pm20) REVERT: A 145 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: A 305 GLU cc_start: 0.7539 (tp30) cc_final: 0.7269 (tm-30) REVERT: A 601 GLU cc_start: 0.6539 (mm-30) cc_final: 0.5855 (mm-30) REVERT: A 606 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6233 (mtp85) REVERT: A 629 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7307 (ttm110) outliers start: 29 outliers final: 11 residues processed: 143 average time/residue: 1.7033 time to fit residues: 259.9230 Evaluate side-chains 147 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.275 ------------------------------------------------------------------------------- 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 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 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 116 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 56 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11490 Z= 0.191 Angle : 0.501 4.686 15482 Z= 0.273 Chirality : 0.040 0.168 1670 Planarity : 0.004 0.035 1902 Dihedral : 21.113 174.688 2034 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.50 % Allowed : 7.05 % Favored : 90.45 % 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: 1.90 (0.24), residues: 1288 helix: 2.19 (0.17), residues: 890 sheet: 0.92 (0.75), residues: 44 loop : -1.19 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 227 HIS 0.008 0.001 HIS B 619 PHE 0.011 0.002 PHE B 181 TYR 0.013 0.002 TYR B 589 ARG 0.003 0.000 ARG A 170 *********************** 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: 28 poor density : 136 time to evaluate : 1.322 Fit side-chains REVERT: B 42 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7049 (mm-30) REVERT: B 69 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7436 (mttm) REVERT: B 102 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: B 145 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: B 305 GLU cc_start: 0.7494 (tp30) cc_final: 0.7183 (tm-30) REVERT: B 325 THR cc_start: 0.7930 (t) cc_final: 0.7556 (m) REVERT: B 601 GLU cc_start: 0.6552 (mm-30) cc_final: 0.5878 (mm-30) REVERT: B 606 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6227 (mtp85) REVERT: B 629 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7342 (ttm110) REVERT: A 42 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6996 (mm-30) REVERT: A 102 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: A 145 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: A 305 GLU cc_start: 0.7478 (tp30) cc_final: 0.7166 (tm-30) REVERT: A 325 THR cc_start: 0.7905 (t) cc_final: 0.7559 (m) REVERT: A 601 GLU cc_start: 0.6538 (mm-30) cc_final: 0.5875 (mm-30) REVERT: A 606 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6225 (mtp85) REVERT: A 629 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7342 (ttm110) REVERT: A 647 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7233 (tpt170) REVERT: A 703 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6029 (tp30) outliers start: 28 outliers final: 10 residues processed: 145 average time/residue: 1.7722 time to fit residues: 273.7467 Evaluate side-chains 153 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 11490 Z= 0.399 Angle : 0.698 6.111 15482 Z= 0.375 Chirality : 0.049 0.228 1670 Planarity : 0.006 0.046 1902 Dihedral : 21.799 168.899 2034 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 8.21 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.37 (0.24), residues: 1288 helix: 1.79 (0.17), residues: 890 sheet: 1.01 (0.75), residues: 44 loop : -1.44 (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 B 619 PHE 0.024 0.003 PHE B 419 TYR 0.023 0.003 TYR A 352 ARG 0.005 0.001 ARG B 250 *********************** 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 164 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.134 Fit side-chains REVERT: B 42 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7068 (mm-30) REVERT: B 69 LYS cc_start: 0.7649 (mtmm) cc_final: 0.7436 (mttm) REVERT: B 102 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: B 145 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: B 305 GLU cc_start: 0.7534 (tp30) cc_final: 0.7214 (tm-30) REVERT: B 325 THR cc_start: 0.8028 (t) cc_final: 0.7762 (m) REVERT: B 601 GLU cc_start: 0.6640 (mm-30) cc_final: 0.5989 (mm-30) REVERT: B 629 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7333 (ttm110) REVERT: B 647 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7181 (tpt170) REVERT: B 703 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6402 (mp0) REVERT: A 42 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6982 (mm-30) REVERT: A 102 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6408 (pm20) REVERT: A 145 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: A 305 GLU cc_start: 0.7530 (tp30) cc_final: 0.7210 (tm-30) REVERT: A 325 THR cc_start: 0.8034 (t) cc_final: 0.7766 (m) REVERT: A 495 THR cc_start: 0.8093 (t) cc_final: 0.7757 (m) REVERT: A 544 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 601 GLU cc_start: 0.6652 (mm-30) cc_final: 0.5999 (mm-30) REVERT: A 629 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7336 (ttm110) REVERT: A 703 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6088 (tp30) outliers start: 25 outliers final: 10 residues processed: 147 average time/residue: 1.7016 time to fit residues: 266.8023 Evaluate side-chains 156 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.317 ------------------------------------------------------------------------------- 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 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 629 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.0570 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11490 Z= 0.188 Angle : 0.510 4.823 15482 Z= 0.280 Chirality : 0.040 0.173 1670 Planarity : 0.004 0.036 1902 Dihedral : 20.227 153.194 2034 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.05 % Allowed : 8.75 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.24), residues: 1288 helix: 2.16 (0.17), residues: 890 sheet: 1.14 (0.79), residues: 44 loop : -1.32 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 227 HIS 0.008 0.001 HIS A 619 PHE 0.012 0.002 PHE B 223 TYR 0.013 0.002 TYR B 589 ARG 0.002 0.000 ARG A 170 *********************** 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 166 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.265 Fit side-chains REVERT: B 69 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7455 (mttm) REVERT: B 102 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: B 145 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: B 305 GLU cc_start: 0.7498 (tp30) cc_final: 0.7186 (tm-30) REVERT: B 325 THR cc_start: 0.8000 (t) cc_final: 0.7728 (m) REVERT: B 601 GLU cc_start: 0.6577 (mm-30) cc_final: 0.5935 (mm-30) REVERT: B 606 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6215 (mtp85) REVERT: B 629 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7352 (ttm110) REVERT: B 647 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7176 (tpt170) REVERT: A 42 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6986 (mm-30) REVERT: A 100 LYS cc_start: 0.7211 (tptt) cc_final: 0.6768 (pttp) REVERT: A 102 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6398 (pm20) REVERT: A 145 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: A 305 GLU cc_start: 0.7492 (tp30) cc_final: 0.7180 (tm-30) REVERT: A 325 THR cc_start: 0.8004 (t) cc_final: 0.7739 (m) REVERT: A 495 THR cc_start: 0.8057 (t) cc_final: 0.7732 (m) REVERT: A 544 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 601 GLU cc_start: 0.6581 (mm-30) cc_final: 0.5937 (mm-30) REVERT: A 606 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6227 (mtp85) REVERT: A 629 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7354 (ttm110) REVERT: A 703 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6044 (tp30) outliers start: 23 outliers final: 9 residues processed: 150 average time/residue: 1.7582 time to fit residues: 280.5570 Evaluate side-chains 157 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 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 57 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 105 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 2.7484 ------------------------------------------------------------------------------- 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 A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11490 Z= 0.287 Angle : 0.606 5.328 15482 Z= 0.329 Chirality : 0.045 0.197 1670 Planarity : 0.005 0.040 1902 Dihedral : 20.489 154.638 2034 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.88 % Allowed : 9.11 % 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: 1.59 (0.24), residues: 1288 helix: 1.97 (0.17), residues: 890 sheet: 1.16 (0.78), residues: 44 loop : -1.41 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 227 HIS 0.012 0.002 HIS B 619 PHE 0.017 0.002 PHE B 419 TYR 0.019 0.003 TYR B 589 ARG 0.004 0.001 ARG A 250 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2576 Ramachandran restraints generated. 1288 Oldfield, 0 Emsley, 1288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 1.356 Fit side-chains REVERT: B 42 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 69 LYS cc_start: 0.7658 (mtmm) cc_final: 0.7446 (mttm) REVERT: B 102 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6378 (pm20) REVERT: B 145 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: B 305 GLU cc_start: 0.7523 (tp30) cc_final: 0.7231 (tm-30) REVERT: B 325 THR cc_start: 0.8045 (t) cc_final: 0.7790 (m) REVERT: B 601 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5973 (mm-30) REVERT: B 629 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7320 (ttm110) REVERT: B 647 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7171 (tpt170) REVERT: A 42 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6998 (mm-30) REVERT: A 102 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6386 (pm20) REVERT: A 145 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: A 305 GLU cc_start: 0.7516 (tp30) cc_final: 0.7224 (tm-30) REVERT: A 325 THR cc_start: 0.8045 (t) cc_final: 0.7794 (m) REVERT: A 495 THR cc_start: 0.8083 (t) cc_final: 0.7767 (m) REVERT: A 544 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 601 GLU cc_start: 0.6626 (mm-30) cc_final: 0.5974 (mm-30) REVERT: A 606 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6266 (mtp85) REVERT: A 629 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7322 (ttm110) REVERT: A 703 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6336 (tp30) outliers start: 21 outliers final: 9 residues processed: 146 average time/residue: 1.7491 time to fit residues: 271.7891 Evaluate side-chains 155 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3542 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= 0.237 Angle : 0.554 4.949 15482 Z= 0.302 Chirality : 0.042 0.185 1670 Planarity : 0.005 0.038 1902 Dihedral : 19.731 145.577 2034 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.88 % Allowed : 9.20 % 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: 1.75 (0.24), residues: 1288 helix: 2.10 (0.17), residues: 890 sheet: 1.24 (0.80), residues: 44 loop : -1.37 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 227 HIS 0.010 0.001 HIS B 619 PHE 0.014 0.002 PHE B 223 TYR 0.016 0.002 TYR B 589 ARG 0.003 0.001 ARG B 170 *********************** 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 161 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.310 Fit side-chains REVERT: B 69 LYS cc_start: 0.7647 (mtmm) cc_final: 0.7423 (mttm) REVERT: B 100 LYS cc_start: 0.7200 (tptt) cc_final: 0.6757 (pttp) REVERT: B 102 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: B 145 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: B 305 GLU cc_start: 0.7507 (tp30) cc_final: 0.7197 (tm-30) REVERT: B 325 THR cc_start: 0.8029 (t) cc_final: 0.7778 (m) REVERT: B 599 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6827 (t0) REVERT: B 601 GLU cc_start: 0.6594 (mm-30) cc_final: 0.5954 (mm-30) REVERT: B 629 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7340 (ttm110) REVERT: B 647 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7165 (tpt170) REVERT: B 703 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6087 (tp30) REVERT: A 42 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7010 (mm-30) REVERT: A 100 LYS cc_start: 0.7202 (tptt) cc_final: 0.6772 (pttp) REVERT: A 102 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6375 (pm20) REVERT: A 145 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: A 305 GLU cc_start: 0.7500 (tp30) cc_final: 0.7191 (tm-30) REVERT: A 325 THR cc_start: 0.8031 (t) cc_final: 0.7788 (m) REVERT: A 495 THR cc_start: 0.8067 (t) cc_final: 0.7763 (m) REVERT: A 544 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 599 ASN cc_start: 0.7105 (OUTLIER) cc_final: 0.6845 (t0) REVERT: A 601 GLU cc_start: 0.6594 (mm-30) cc_final: 0.5948 (mm-30) REVERT: A 606 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6241 (mtp85) REVERT: A 629 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7342 (ttm110) REVERT: A 703 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6287 (tp30) outliers start: 21 outliers final: 11 residues processed: 145 average time/residue: 1.8363 time to fit residues: 283.0781 Evaluate side-chains 159 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 599 ASN 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 57 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG 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 109 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 11490 Z= 0.288 Angle : 0.603 5.465 15482 Z= 0.327 Chirality : 0.044 0.197 1670 Planarity : 0.005 0.040 1902 Dihedral : 19.955 147.181 2034 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.14 % Allowed : 9.11 % 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: 1.61 (0.24), residues: 1288 helix: 1.99 (0.17), residues: 890 sheet: 1.24 (0.79), residues: 44 loop : -1.44 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 227 HIS 0.011 0.002 HIS B 619 PHE 0.016 0.002 PHE B 419 TYR 0.020 0.003 TYR A 432 ARG 0.004 0.001 ARG A 170 *********************** 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: 24 poor density : 137 time to evaluate : 1.172 Fit side-chains REVERT: B 42 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7042 (mm-30) REVERT: B 69 LYS cc_start: 0.7651 (mtmm) cc_final: 0.7436 (mttm) REVERT: B 100 LYS cc_start: 0.7175 (tptt) cc_final: 0.6745 (pttp) REVERT: B 102 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6429 (pm20) REVERT: B 145 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: B 305 GLU cc_start: 0.7518 (tp30) cc_final: 0.7228 (tm-30) REVERT: B 325 THR cc_start: 0.8049 (t) cc_final: 0.7803 (m) REVERT: B 599 ASN cc_start: 0.7031 (OUTLIER) cc_final: 0.6696 (t0) REVERT: B 601 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5969 (mm-30) REVERT: B 606 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6277 (mtp85) REVERT: B 629 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7317 (ttm110) REVERT: B 647 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7173 (tpt170) REVERT: B 703 GLU cc_start: 0.6763 (mm-30) cc_final: 0.6072 (tp30) REVERT: A 42 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7017 (mm-30) REVERT: A 100 LYS cc_start: 0.7169 (tptt) cc_final: 0.6749 (pttp) REVERT: A 102 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6405 (pm20) REVERT: A 104 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7229 (tt0) REVERT: A 145 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: A 305 GLU cc_start: 0.7510 (tp30) cc_final: 0.7221 (tm-30) REVERT: A 325 THR cc_start: 0.8042 (t) cc_final: 0.7799 (m) REVERT: A 495 THR cc_start: 0.8090 (t) cc_final: 0.7785 (m) REVERT: A 544 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8524 (tt) REVERT: A 599 ASN cc_start: 0.7032 (OUTLIER) cc_final: 0.6702 (t0) REVERT: A 601 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5956 (mm-30) REVERT: A 606 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6264 (mtp85) REVERT: A 629 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7319 (ttm110) REVERT: A 703 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6323 (tp30) outliers start: 24 outliers final: 8 residues processed: 145 average time/residue: 1.8473 time to fit residues: 284.5885 Evaluate side-chains 157 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 599 ASN Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3572 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= 0.253 Angle : 0.574 5.271 15482 Z= 0.313 Chirality : 0.043 0.187 1670 Planarity : 0.005 0.039 1902 Dihedral : 19.753 147.213 2034 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.61 % Allowed : 9.64 % 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: 1.68 (0.24), residues: 1288 helix: 2.05 (0.17), residues: 890 sheet: 1.25 (0.79), residues: 44 loop : -1.45 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 227 HIS 0.010 0.001 HIS B 619 PHE 0.016 0.002 PHE A 419 TYR 0.018 0.002 TYR A 432 ARG 0.003 0.001 ARG B 170 ********************** 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: 18 poor density : 137 time to evaluate : 1.421 Fit side-chains REVERT: B 69 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7431 (mttm) REVERT: B 100 LYS cc_start: 0.7182 (tptt) cc_final: 0.6748 (pttp) REVERT: B 102 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6437 (pm20) REVERT: B 145 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6066 (mp0) REVERT: B 305 GLU cc_start: 0.7509 (tp30) cc_final: 0.7223 (tm-30) REVERT: B 325 THR cc_start: 0.8052 (t) cc_final: 0.7807 (m) REVERT: B 601 GLU cc_start: 0.6601 (mm-30) cc_final: 0.5966 (mm-30) REVERT: B 606 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6247 (mtp85) REVERT: B 629 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7317 (ttm110) REVERT: B 647 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7169 (tpt170) REVERT: B 703 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6109 (tp30) REVERT: A 42 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7012 (mm-30) REVERT: A 100 LYS cc_start: 0.7181 (tptt) cc_final: 0.6759 (pttp) REVERT: A 102 GLN cc_start: 0.7350 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: A 145 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6123 (mp0) REVERT: A 305 GLU cc_start: 0.7504 (tp30) cc_final: 0.7217 (tm-30) REVERT: A 325 THR cc_start: 0.8045 (t) cc_final: 0.7800 (m) REVERT: A 495 THR cc_start: 0.8087 (t) cc_final: 0.7787 (m) REVERT: A 544 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8488 (tp) REVERT: A 601 GLU cc_start: 0.6602 (mm-30) cc_final: 0.5967 (mm-30) REVERT: A 606 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6249 (mtp85) REVERT: A 629 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7316 (ttm110) REVERT: A 703 GLU cc_start: 0.6858 (mm-30) cc_final: 0.6355 (tp30) outliers start: 18 outliers final: 8 residues processed: 141 average time/residue: 1.9064 time to fit residues: 284.8585 Evaluate side-chains 154 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 102 GLN Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 606 ARG Chi-restraints excluded: chain B residue 629 ARG Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 606 ARG Chi-restraints excluded: chain A residue 629 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 0.1980 chunk 90 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 599 ASN A 58 ASN A 135 ASN A 599 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.155583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.116535 restraints weight = 9763.832| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.10 r_work: 0.3053 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3583 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= 0.150 Angle : 0.471 4.623 15482 Z= 0.259 Chirality : 0.039 0.161 1670 Planarity : 0.004 0.035 1902 Dihedral : 18.267 143.790 2034 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.61 % Allowed : 9.73 % 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: 2.09 (0.24), residues: 1288 helix: 2.40 (0.17), residues: 890 sheet: 1.34 (0.83), residues: 44 loop : -1.38 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 227 HIS 0.007 0.001 HIS B 619 PHE 0.010 0.001 PHE A 223 TYR 0.012 0.002 TYR A 589 ARG 0.002 0.000 ARG A 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4836.85 seconds wall clock time: 88 minutes 24.82 seconds (5304.82 seconds total)