Starting phenix.real_space_refine on Thu Jul 2 05:14:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wi0_32517/07_2026/7wi0_32517.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4303 2.51 5 N 1148 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6823 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 940 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 935 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 800 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.22 Number of scatterers: 6823 At special positions: 0 Unit cell: (86.358, 94.916, 122.146, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1342 8.00 N 1148 7.00 C 4303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.01 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 336.0 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 22 sheets defined 2.7% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.848A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 3.620A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP C 90 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.807A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.726A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.608A pdb=" N ARG A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.636A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.689A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 73 " --> pdb=" O THR B 78 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 6 through 7 removed outlier: 3.508A pdb=" N LEU C 18 " --> pdb=" O MET C 83 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR C 69 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 7.932A pdb=" N MET C 34 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.722A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 54 removed outlier: 5.405A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 38 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.603A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.674A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.522A pdb=" N GLN E 37 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN E 89 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.909A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.054A pdb=" N GLU H 10 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL H 119 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA H 92 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.506A pdb=" N ASP H 82 " --> pdb=" O THR H 69 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.561A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 9 through 11 removed outlier: 3.646A pdb=" N TYR L 88 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 107 " --> pdb=" O ALA L 86 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA L 86 " --> pdb=" O VAL L 107 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER L 92 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 17 through 21 158 hydrogen bonds defined for protein. 384 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: 0.83 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1101 1.26 - 1.40: 1858 1.40 - 1.54: 3952 1.54 - 1.68: 39 1.68 - 1.83: 40 Bond restraints: 6990 Sorted by residual: bond pdb=" C THR C 78 " pdb=" O THR C 78 " ideal model delta sigma weight residual 1.234 1.462 -0.228 1.22e-02 6.72e+03 3.49e+02 bond pdb=" C SER B 106 " pdb=" O SER B 106 " ideal model delta sigma weight residual 1.234 1.117 0.117 1.19e-02 7.06e+03 9.66e+01 bond pdb=" C VAL B 101 " pdb=" O VAL B 101 " ideal model delta sigma weight residual 1.235 1.150 0.084 1.45e-02 4.76e+03 3.38e+01 bond pdb=" CA SER B 106 " pdb=" C SER B 106 " ideal model delta sigma weight residual 1.521 1.452 0.069 1.22e-02 6.72e+03 3.22e+01 bond pdb=" C THR C 78 " pdb=" N LEU C 79 " ideal model delta sigma weight residual 1.331 1.401 -0.070 1.29e-02 6.01e+03 2.94e+01 ... (remaining 6985 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 9380 3.67 - 7.34: 101 7.34 - 11.01: 15 11.01 - 14.68: 1 14.68 - 18.36: 2 Bond angle restraints: 9499 Sorted by residual: angle pdb=" N GLY B 105 " pdb=" CA GLY B 105 " pdb=" C GLY B 105 " ideal model delta sigma weight residual 112.49 130.85 -18.36 1.21e+00 6.83e-01 2.30e+02 angle pdb=" N VAL B 101 " pdb=" CA VAL B 101 " pdb=" C VAL B 101 " ideal model delta sigma weight residual 112.29 121.27 -8.98 9.40e-01 1.13e+00 9.12e+01 angle pdb=" N ASP B 112 " pdb=" CA ASP B 112 " pdb=" C ASP B 112 " ideal model delta sigma weight residual 111.36 120.42 -9.06 1.09e+00 8.42e-01 6.91e+01 angle pdb=" N ALA B 102 " pdb=" CA ALA B 102 " pdb=" C ALA B 102 " ideal model delta sigma weight residual 109.59 98.35 11.24 1.47e+00 4.63e-01 5.85e+01 angle pdb=" O SER B 106 " pdb=" C SER B 106 " pdb=" N SER B 107 " ideal model delta sigma weight residual 123.46 116.86 6.60 9.90e-01 1.02e+00 4.44e+01 ... (remaining 9494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 3677 17.97 - 35.95: 346 35.95 - 53.92: 53 53.92 - 71.89: 9 71.89 - 89.87: 8 Dihedral angle restraints: 4093 sinusoidal: 1555 harmonic: 2538 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 149.43 -56.43 1 1.00e+01 1.00e-02 4.29e+01 dihedral pdb=" CA SER E 93 " pdb=" C SER E 93 " pdb=" N TYR E 94 " pdb=" CA TYR E 94 " ideal model delta harmonic sigma weight residual -180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual -86.00 -121.59 35.59 1 1.00e+01 1.00e-02 1.79e+01 ... (remaining 4090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 916 0.095 - 0.189: 97 0.189 - 0.284: 13 0.284 - 0.379: 1 0.379 - 0.474: 1 Chirality restraints: 1028 Sorted by residual: chirality pdb=" CA VAL B 101 " pdb=" N VAL B 101 " pdb=" C VAL B 101 " pdb=" CB VAL B 101 " both_signs ideal model delta sigma weight residual False 2.44 1.97 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CA SER B 107 " pdb=" N SER B 107 " pdb=" C SER B 107 " pdb=" CB SER B 107 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA TYR E 94 " pdb=" N TYR E 94 " pdb=" C TYR E 94 " pdb=" CB TYR E 94 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 1025 not shown) Planarity restraints: 1227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 77 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ASN C 77 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN C 77 " 0.018 2.00e-02 2.50e+03 pdb=" N THR C 78 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.043 5.00e-02 4.00e+02 6.40e-02 6.56e+00 pdb=" N PRO A 373 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.042 5.00e-02 4.00e+02 6.34e-02 6.43e+00 pdb=" N PRO L 46 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.035 5.00e-02 4.00e+02 ... (remaining 1224 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1858 2.79 - 3.32: 5543 3.32 - 3.85: 10966 3.85 - 4.37: 11967 4.37 - 4.90: 21668 Nonbonded interactions: 52002 Sorted by model distance: nonbonded pdb=" OE1 GLN H 6 " pdb=" OG1 THR H 117 " model vdw 2.265 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.272 3.040 nonbonded pdb=" OG SER D 63 " pdb=" O THR D 74 " model vdw 2.314 3.040 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.315 3.040 nonbonded pdb=" OD1 ASP B 90 " pdb=" OH TYR B 94 " model vdw 2.317 3.040 ... (remaining 51997 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 'D' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) selection = (chain 'E' and (resid 1 through 8 or resid 10 through 30 or resid 33 or resid 35 \ through 49 or resid 52 through 54 or resid 56 through 69 or resid 71 through 80 \ or resid 82 through 90 or resid 93 or resid 98 through 103 or resid 105 through \ 107)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 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 0.228 6998 Z= 0.490 Angle : 1.049 18.355 9516 Z= 0.635 Chirality : 0.064 0.474 1028 Planarity : 0.007 0.064 1226 Dihedral : 14.399 89.866 2466 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.60 % Favored : 91.28 % Rotamer: Outliers : 0.40 % Allowed : 10.08 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.24), residues: 872 helix: -5.25 (0.15), residues: 30 sheet: -2.73 (0.25), residues: 349 loop : -2.85 (0.23), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 61 TYR 0.023 0.002 TYR C 95 PHE 0.019 0.002 PHE B 27 TRP 0.017 0.002 TRP B 114 HIS 0.005 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00799 / 0.49 ( 6990) covalent geometry : angle 1.04817 / 0.64 ( 9499) SS BOND : bond 0.00810 / 0.41 ( 7) SS BOND : angle 1.30821 / 0.92 ( 14) hydrogen bonds : bond 0.30229 / 19.22 ( 155) hydrogen bonds : angle 10.94885 / 7.51 ( 384) link_NAG-ASN : bond 0.00220 / 0.12 ( 1) link_NAG-ASN : angle 1.84521 / 1.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 226 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7453 (ttpt) REVERT: B 50 VAL cc_start: 0.9168 (p) cc_final: 0.8790 (p) REVERT: B 51 MET cc_start: 0.8872 (mmm) cc_final: 0.8487 (mmt) REVERT: B 116 GLN cc_start: 0.8414 (tp40) cc_final: 0.8188 (mm-40) REVERT: C 65 LYS cc_start: 0.7983 (ptpt) cc_final: 0.7655 (ttpt) REVERT: C 76 LYS cc_start: 0.8675 (mtpp) cc_final: 0.8424 (mtpp) REVERT: E 2 ILE cc_start: 0.7706 (mp) cc_final: 0.7210 (mp) REVERT: E 85 THR cc_start: 0.8060 (t) cc_final: 0.7838 (m) REVERT: E 90 GLN cc_start: 0.8712 (pp30) cc_final: 0.8374 (pp30) REVERT: H 62 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8252 (tm-30) REVERT: H 89 GLU cc_start: 0.7658 (mp0) cc_final: 0.7446 (mt-10) REVERT: L 53 ASN cc_start: 0.7528 (m-40) cc_final: 0.7328 (t0) REVERT: L 63 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7774 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 227 average time/residue: 0.0675 time to fit residues: 20.1608 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 HIS D 31 ASN E 37 GLN L 1 GLN L 36 HIS L 39 GLN L 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108073 restraints weight = 11753.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111270 restraints weight = 7023.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.113510 restraints weight = 4949.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115052 restraints weight = 3862.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.116006 restraints weight = 3239.226| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6998 Z= 0.124 Angle : 0.630 8.270 9516 Z= 0.333 Chirality : 0.045 0.176 1028 Planarity : 0.005 0.049 1226 Dihedral : 5.371 36.937 980 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.75 % Allowed : 18.82 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.55 (0.26), residues: 872 helix: -5.03 (0.17), residues: 24 sheet: -2.27 (0.26), residues: 354 loop : -2.26 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 24 TYR 0.026 0.001 TYR L 51 PHE 0.022 0.001 PHE B 29 TRP 0.031 0.001 TRP B 47 HIS 0.004 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6990) covalent geometry : angle 0.62934 / 0.33 ( 9499) SS BOND : bond 0.00342 / 0.18 ( 7) SS BOND : angle 1.07240 / 0.71 ( 14) hydrogen bonds : bond 0.04331 / 2.51 ( 155) hydrogen bonds : angle 6.94804 / 4.79 ( 384) link_NAG-ASN : bond 0.00038 / 0.02 ( 1) link_NAG-ASN : angle 0.98532 / 0.57 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8235 (t60) cc_final: 0.7726 (t60) REVERT: C 36 TRP cc_start: 0.7865 (m100) cc_final: 0.7541 (m100) REVERT: C 65 LYS cc_start: 0.7930 (ptpt) cc_final: 0.7563 (ttpt) REVERT: E 78 LEU cc_start: 0.8141 (mm) cc_final: 0.7813 (tt) REVERT: E 90 GLN cc_start: 0.8782 (pp30) cc_final: 0.8305 (pp30) REVERT: H 43 GLN cc_start: 0.8519 (mp10) cc_final: 0.7930 (mp10) REVERT: H 87 ARG cc_start: 0.6951 (mtm110) cc_final: 0.6616 (mtm110) REVERT: L 63 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7586 (ttp-110) outliers start: 13 outliers final: 2 residues processed: 207 average time/residue: 0.0681 time to fit residues: 18.7541 Evaluate side-chains 173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.0050 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 53 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN H 6 GLN H 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107197 restraints weight = 11866.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110325 restraints weight = 7204.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.112523 restraints weight = 5137.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114007 restraints weight = 4052.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115052 restraints weight = 3430.283| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6998 Z= 0.124 Angle : 0.609 8.383 9516 Z= 0.318 Chirality : 0.044 0.177 1028 Planarity : 0.005 0.053 1226 Dihedral : 4.872 31.703 975 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.15 % Allowed : 21.77 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.28), residues: 872 helix: -5.09 (0.18), residues: 24 sheet: -1.92 (0.27), residues: 355 loop : -1.93 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 87 TYR 0.027 0.001 TYR L 51 PHE 0.011 0.001 PHE B 29 TRP 0.019 0.001 TRP B 47 HIS 0.003 0.001 HIS H 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 6990) covalent geometry : angle 0.60738 / 0.32 ( 9499) SS BOND : bond 0.00281 / 0.16 ( 7) SS BOND : angle 1.22916 / 0.79 ( 14) hydrogen bonds : bond 0.03420 / 1.99 ( 155) hydrogen bonds : angle 6.22053 / 4.27 ( 384) link_NAG-ASN : bond 0.00085 / 0.04 ( 1) link_NAG-ASN : angle 0.86581 / 0.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8196 (t60) cc_final: 0.7623 (t60) REVERT: C 36 TRP cc_start: 0.7796 (m100) cc_final: 0.7574 (m100) REVERT: C 46 GLU cc_start: 0.7778 (tt0) cc_final: 0.7540 (pt0) REVERT: C 65 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7559 (ttpt) REVERT: C 86 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7905 (pp) REVERT: E 90 GLN cc_start: 0.8817 (pp30) cc_final: 0.8273 (pp30) REVERT: H 43 GLN cc_start: 0.8528 (mp10) cc_final: 0.7943 (mp10) REVERT: L 63 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7627 (mtp-110) outliers start: 16 outliers final: 6 residues processed: 185 average time/residue: 0.0680 time to fit residues: 16.6794 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 55 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 505 HIS B 39 GLN D 38 GLN E 100 GLN H 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.104601 restraints weight = 12107.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.107642 restraints weight = 7403.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109786 restraints weight = 5320.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.111220 restraints weight = 4219.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112108 restraints weight = 3596.360| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6998 Z= 0.171 Angle : 0.640 8.031 9516 Z= 0.330 Chirality : 0.045 0.218 1028 Planarity : 0.005 0.087 1226 Dihedral : 4.900 31.126 975 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.36 % Allowed : 22.85 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.28), residues: 872 helix: -5.02 (0.17), residues: 30 sheet: -1.83 (0.26), residues: 366 loop : -1.82 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 346 TYR 0.022 0.001 TYR L 51 PHE 0.010 0.001 PHE D 71 TRP 0.017 0.001 TRP B 47 HIS 0.004 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 6990) covalent geometry : angle 0.63881 / 0.33 ( 9499) SS BOND : bond 0.00343 / 0.18 ( 7) SS BOND : angle 1.28276 / 0.78 ( 14) hydrogen bonds : bond 0.03469 / 2.01 ( 155) hydrogen bonds : angle 6.03361 / 4.20 ( 384) link_NAG-ASN : bond 0.00123 / 0.06 ( 1) link_NAG-ASN : angle 1.22184 / 0.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8276 (t60) cc_final: 0.7784 (t60) REVERT: B 109 ASP cc_start: 0.8485 (t70) cc_final: 0.8194 (t70) REVERT: C 36 TRP cc_start: 0.7845 (m100) cc_final: 0.7509 (m100) REVERT: C 65 LYS cc_start: 0.7964 (ptpt) cc_final: 0.7637 (ttpt) REVERT: C 86 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8017 (pp) REVERT: E 37 GLN cc_start: 0.7351 (tt0) cc_final: 0.6782 (tt0) REVERT: E 90 GLN cc_start: 0.8844 (pp30) cc_final: 0.8372 (pp30) REVERT: H 43 GLN cc_start: 0.8607 (mp10) cc_final: 0.8076 (mp10) REVERT: H 63 LYS cc_start: 0.8790 (tttp) cc_final: 0.8341 (ttpp) REVERT: L 63 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7385 (ttp-110) outliers start: 25 outliers final: 19 residues processed: 181 average time/residue: 0.0643 time to fit residues: 15.6364 Evaluate side-chains 178 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN E 100 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103699 restraints weight = 12011.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106708 restraints weight = 7315.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108846 restraints weight = 5245.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110268 restraints weight = 4154.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.111206 restraints weight = 3538.405| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6998 Z= 0.161 Angle : 0.630 9.182 9516 Z= 0.321 Chirality : 0.044 0.218 1028 Planarity : 0.004 0.051 1226 Dihedral : 4.846 30.289 975 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.57 % Allowed : 22.85 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.27), residues: 872 helix: -4.95 (0.21), residues: 18 sheet: -1.83 (0.26), residues: 371 loop : -1.67 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 87 TYR 0.020 0.001 TYR E 94 PHE 0.010 0.001 PHE L 64 TRP 0.018 0.001 TRP B 47 HIS 0.004 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6990) covalent geometry : angle 0.62846 / 0.32 ( 9499) SS BOND : bond 0.00292 / 0.15 ( 7) SS BOND : angle 1.30785 / 0.77 ( 14) hydrogen bonds : bond 0.03295 / 1.88 ( 155) hydrogen bonds : angle 5.77183 / 4.03 ( 384) link_NAG-ASN : bond 0.00048 / 0.03 ( 1) link_NAG-ASN : angle 1.21331 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.182 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8225 (t60) cc_final: 0.7778 (t60) REVERT: B 109 ASP cc_start: 0.8458 (t70) cc_final: 0.8219 (t70) REVERT: C 36 TRP cc_start: 0.7920 (m100) cc_final: 0.7545 (m100) REVERT: C 65 LYS cc_start: 0.8020 (ptpt) cc_final: 0.7703 (ttpt) REVERT: C 86 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8091 (pp) REVERT: E 90 GLN cc_start: 0.8753 (pp30) cc_final: 0.8062 (pp30) REVERT: H 43 GLN cc_start: 0.8602 (mp10) cc_final: 0.8065 (mp10) REVERT: H 73 ASP cc_start: 0.7761 (t0) cc_final: 0.7440 (t0) REVERT: L 63 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7518 (ttp-110) outliers start: 34 outliers final: 24 residues processed: 191 average time/residue: 0.0538 time to fit residues: 14.1131 Evaluate side-chains 184 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 85 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.102116 restraints weight = 12200.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105151 restraints weight = 7284.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107336 restraints weight = 5165.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108872 restraints weight = 4048.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.109856 restraints weight = 3398.803| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6998 Z= 0.125 Angle : 0.636 8.690 9516 Z= 0.320 Chirality : 0.044 0.185 1028 Planarity : 0.004 0.049 1226 Dihedral : 4.717 28.012 975 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 3.49 % Allowed : 25.13 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.28), residues: 872 helix: -4.87 (0.20), residues: 18 sheet: -1.66 (0.26), residues: 368 loop : -1.58 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 87 TYR 0.022 0.001 TYR C 80 PHE 0.009 0.001 PHE L 64 TRP 0.015 0.001 TRP B 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 ( 6990) covalent geometry : angle 0.63524 / 0.32 ( 9499) SS BOND : bond 0.00309 / 0.16 ( 7) SS BOND : angle 1.06307 / 0.62 ( 14) hydrogen bonds : bond 0.03076 / 1.77 ( 155) hydrogen bonds : angle 5.57841 / 3.91 ( 384) link_NAG-ASN : bond 0.00080 / 0.04 ( 1) link_NAG-ASN : angle 1.01815 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8120 (t60) cc_final: 0.7724 (t60) REVERT: B 109 ASP cc_start: 0.8474 (t70) cc_final: 0.8252 (t70) REVERT: C 36 TRP cc_start: 0.7842 (m100) cc_final: 0.7439 (m100) REVERT: C 65 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7691 (ttpt) REVERT: C 86 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8060 (pp) REVERT: E 90 GLN cc_start: 0.8743 (pp30) cc_final: 0.8231 (pp30) REVERT: H 43 GLN cc_start: 0.8579 (mp10) cc_final: 0.8022 (mp10) REVERT: H 73 ASP cc_start: 0.7828 (t0) cc_final: 0.7406 (t0) REVERT: L 63 ARG cc_start: 0.8029 (mtm-85) cc_final: 0.7684 (ttp-110) REVERT: L 81 GLN cc_start: 0.7988 (mp10) cc_final: 0.7777 (mp10) outliers start: 26 outliers final: 19 residues processed: 179 average time/residue: 0.0622 time to fit residues: 15.1043 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 79 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.2368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105249 restraints weight = 11918.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108310 restraints weight = 6916.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110436 restraints weight = 4803.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111779 restraints weight = 3723.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.112891 restraints weight = 3138.034| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6998 Z= 0.102 Angle : 0.620 8.810 9516 Z= 0.311 Chirality : 0.043 0.150 1028 Planarity : 0.004 0.050 1226 Dihedral : 4.495 23.042 975 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.36 % Allowed : 25.67 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.28), residues: 872 helix: -4.86 (0.26), residues: 12 sheet: -1.41 (0.27), residues: 369 loop : -1.58 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.018 0.001 TYR E 94 PHE 0.035 0.001 PHE B 29 TRP 0.015 0.001 TRP B 47 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6990) covalent geometry : angle 0.61946 / 0.31 ( 9499) SS BOND : bond 0.00383 / 0.20 ( 7) SS BOND : angle 0.97307 / 0.58 ( 14) hydrogen bonds : bond 0.02807 / 1.59 ( 155) hydrogen bonds : angle 5.41592 / 3.81 ( 384) link_NAG-ASN : bond 0.00163 / 0.09 ( 1) link_NAG-ASN : angle 0.79777 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.231 Fit side-chains REVERT: B 47 TRP cc_start: 0.7994 (t60) cc_final: 0.7693 (t60) REVERT: B 82 GLU cc_start: 0.7690 (tp30) cc_final: 0.7376 (mm-30) REVERT: C 36 TRP cc_start: 0.7840 (m100) cc_final: 0.7469 (m100) REVERT: C 65 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7688 (ttpt) REVERT: C 86 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8016 (pp) REVERT: C 103 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: E 90 GLN cc_start: 0.8678 (pp30) cc_final: 0.8093 (pp30) REVERT: H 43 GLN cc_start: 0.8559 (mp10) cc_final: 0.8015 (mp10) REVERT: H 73 ASP cc_start: 0.7798 (t0) cc_final: 0.7381 (t0) REVERT: H 89 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8139 (pt0) REVERT: L 63 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7697 (ttp-110) outliers start: 25 outliers final: 15 residues processed: 181 average time/residue: 0.0587 time to fit residues: 14.5945 Evaluate side-chains 173 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.098199 restraints weight = 12218.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.101091 restraints weight = 7374.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103115 restraints weight = 5265.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.104457 restraints weight = 4167.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.105429 restraints weight = 3560.739| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6998 Z= 0.231 Angle : 0.712 8.850 9516 Z= 0.365 Chirality : 0.047 0.251 1028 Planarity : 0.005 0.054 1226 Dihedral : 5.102 29.840 975 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 3.90 % Allowed : 24.73 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.28), residues: 872 helix: -4.72 (0.28), residues: 12 sheet: -1.44 (0.27), residues: 365 loop : -1.58 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 61 TYR 0.025 0.002 TYR C 80 PHE 0.019 0.002 PHE A 490 TRP 0.019 0.002 TRP E 32 HIS 0.005 0.002 HIS L 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 6990) covalent geometry : angle 0.71042 / 0.36 ( 9499) SS BOND : bond 0.00498 / 0.25 ( 7) SS BOND : angle 1.05095 / 0.67 ( 14) hydrogen bonds : bond 0.03560 / 2.07 ( 155) hydrogen bonds : angle 5.65481 / 3.95 ( 384) link_NAG-ASN : bond 0.00065 / 0.03 ( 1) link_NAG-ASN : angle 1.70213 / 0.99 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.197 Fit side-chains REVERT: B 47 TRP cc_start: 0.8268 (t60) cc_final: 0.7851 (t60) REVERT: B 82 GLU cc_start: 0.7694 (tp30) cc_final: 0.7284 (mm-30) REVERT: C 36 TRP cc_start: 0.7941 (m100) cc_final: 0.7450 (m100) REVERT: C 103 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: D 4 MET cc_start: 0.6864 (mtt) cc_final: 0.6549 (mtt) REVERT: E 90 GLN cc_start: 0.8912 (pp30) cc_final: 0.8271 (pp30) REVERT: H 43 GLN cc_start: 0.8594 (mp10) cc_final: 0.8042 (mp10) REVERT: H 73 ASP cc_start: 0.7837 (t0) cc_final: 0.7378 (t0) REVERT: H 89 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8138 (pt0) REVERT: L 63 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7272 (mtp-110) outliers start: 29 outliers final: 25 residues processed: 174 average time/residue: 0.0627 time to fit residues: 14.9817 Evaluate side-chains 177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100290 restraints weight = 11990.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.103293 restraints weight = 6962.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.105456 restraints weight = 4842.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106861 restraints weight = 3754.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107853 restraints weight = 3158.978| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6998 Z= 0.147 Angle : 0.664 8.527 9516 Z= 0.338 Chirality : 0.045 0.197 1028 Planarity : 0.004 0.048 1226 Dihedral : 4.898 27.974 975 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.23 % Allowed : 26.34 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.28), residues: 872 helix: -4.66 (0.30), residues: 12 sheet: -1.34 (0.27), residues: 374 loop : -1.46 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.023 0.001 TYR A 451 PHE 0.014 0.001 PHE A 342 TRP 0.016 0.001 TRP B 47 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 6990) covalent geometry : angle 0.66246 / 0.34 ( 9499) SS BOND : bond 0.00457 / 0.23 ( 7) SS BOND : angle 1.10267 / 0.65 ( 14) hydrogen bonds : bond 0.03159 / 1.81 ( 155) hydrogen bonds : angle 5.45232 / 3.81 ( 384) link_NAG-ASN : bond 0.00078 / 0.04 ( 1) link_NAG-ASN : angle 1.17518 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: B 47 TRP cc_start: 0.8139 (t60) cc_final: 0.7810 (t60) REVERT: B 82 GLU cc_start: 0.7692 (tp30) cc_final: 0.7332 (mm-30) REVERT: C 36 TRP cc_start: 0.7893 (m100) cc_final: 0.7463 (m100) REVERT: C 86 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8041 (pp) REVERT: C 103 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: D 4 MET cc_start: 0.6768 (mtt) cc_final: 0.6495 (mtt) REVERT: E 4 MET cc_start: 0.6320 (mmm) cc_final: 0.5921 (mmt) REVERT: E 90 GLN cc_start: 0.8865 (pp30) cc_final: 0.8468 (pp30) REVERT: H 43 GLN cc_start: 0.8599 (mp10) cc_final: 0.8129 (mp10) REVERT: H 73 ASP cc_start: 0.7807 (t0) cc_final: 0.7392 (t0) REVERT: H 89 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8223 (pt0) REVERT: L 63 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7214 (mtp-110) outliers start: 24 outliers final: 19 residues processed: 176 average time/residue: 0.0636 time to fit residues: 15.0177 Evaluate side-chains 176 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 93 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 30 optimal weight: 0.0010 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 0.0980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 79 GLN H 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.127052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.103011 restraints weight = 11968.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105993 restraints weight = 7255.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.108040 restraints weight = 5182.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.109476 restraints weight = 4114.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110456 restraints weight = 3493.918| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6998 Z= 0.126 Angle : 0.675 11.033 9516 Z= 0.342 Chirality : 0.044 0.171 1028 Planarity : 0.004 0.053 1226 Dihedral : 4.754 24.693 975 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.55 % Allowed : 27.82 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.28), residues: 872 helix: -4.72 (0.26), residues: 13 sheet: -1.25 (0.27), residues: 371 loop : -1.37 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.024 0.001 TYR C 80 PHE 0.044 0.001 PHE C 68 TRP 0.016 0.001 TRP B 47 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 6990) covalent geometry : angle 0.67377 / 0.34 ( 9499) SS BOND : bond 0.00439 / 0.22 ( 7) SS BOND : angle 1.17191 / 0.69 ( 14) hydrogen bonds : bond 0.02951 / 1.69 ( 155) hydrogen bonds : angle 5.41154 / 3.80 ( 384) link_NAG-ASN : bond 0.00165 / 0.09 ( 1) link_NAG-ASN : angle 1.00829 / 0.58 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.209 Fit side-chains REVERT: B 47 TRP cc_start: 0.8047 (t60) cc_final: 0.7831 (t60) REVERT: B 82 GLU cc_start: 0.7625 (tp30) cc_final: 0.7270 (mm-30) REVERT: C 36 TRP cc_start: 0.7840 (m100) cc_final: 0.7486 (m100) REVERT: C 103 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: E 4 MET cc_start: 0.6265 (mmm) cc_final: 0.5873 (mmt) REVERT: E 90 GLN cc_start: 0.8811 (pp30) cc_final: 0.8454 (pp30) REVERT: H 23 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8348 (ttpp) REVERT: H 43 GLN cc_start: 0.8577 (mp10) cc_final: 0.8148 (mp10) REVERT: H 73 ASP cc_start: 0.7789 (t0) cc_final: 0.7399 (t0) REVERT: L 63 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7373 (mtp-110) outliers start: 19 outliers final: 15 residues processed: 169 average time/residue: 0.0673 time to fit residues: 15.3642 Evaluate side-chains 167 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 103 GLN Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain E residue 88 CYS Chi-restraints excluded: chain H residue 28 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.101961 restraints weight = 12064.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104944 restraints weight = 7268.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106999 restraints weight = 5163.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108294 restraints weight = 4094.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.109348 restraints weight = 3498.966| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6998 Z= 0.146 Angle : 0.696 9.463 9516 Z= 0.351 Chirality : 0.044 0.189 1028 Planarity : 0.004 0.049 1226 Dihedral : 4.801 24.414 975 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 2.69 % Allowed : 27.15 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.29), residues: 872 helix: -4.66 (0.28), residues: 13 sheet: -1.24 (0.27), residues: 371 loop : -1.37 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.017 0.001 TYR E 94 PHE 0.038 0.001 PHE C 68 TRP 0.015 0.001 TRP B 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 6990) covalent geometry : angle 0.69452 / 0.35 ( 9499) SS BOND : bond 0.00434 / 0.22 ( 7) SS BOND : angle 1.37536 / 0.79 ( 14) hydrogen bonds : bond 0.03047 / 1.74 ( 155) hydrogen bonds : angle 5.43818 / 3.77 ( 384) link_NAG-ASN : bond 0.00130 / 0.07 ( 1) link_NAG-ASN : angle 1.32489 / 0.76 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1155.06 seconds wall clock time: 20 minutes 42.70 seconds (1242.70 seconds total)