Starting phenix.real_space_refine on Sat Oct 11 11:43:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145.map" model { file = "/net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb7_41145/10_2025/8tb7_41145_trim.cif" } resolution = 2.94 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= -0.001 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1082 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 33 5.16 5 C 4348 2.51 5 N 1130 2.21 5 O 1279 1.98 5 F 2 1.80 5 H 6676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13468 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 5213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5213 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3275 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1746 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3197 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'ZOB': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 2.78, per 1000 atoms: 0.21 Number of scatterers: 13468 At special positions: 0 Unit cell: (74.34, 128.62, 107.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 33 16.00 F 2 9.00 O 1279 8.00 N 1130 7.00 C 4348 6.00 H 6676 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 380 " - pdb=" SG CYS R 414 " distance=2.02 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 405.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 35.7% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'R' and resid 54 through 78 removed outlier: 3.814A pdb=" N MET R 58 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 108 removed outlier: 4.118A pdb=" N MET R 103 " --> pdb=" O ALA R 99 " (cutoff:3.500A) Proline residue: R 104 - end of helix Processing helix chain 'R' and resid 125 through 155 removed outlier: 3.729A pdb=" N PHE R 129 " --> pdb=" O ARG R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 156 through 160 removed outlier: 3.608A pdb=" N TYR R 159 " --> pdb=" O PRO R 156 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU R 160 " --> pdb=" O MET R 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 156 through 160' Processing helix chain 'R' and resid 164 through 185 removed outlier: 3.681A pdb=" N VAL R 168 " --> pdb=" O THR R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 216 through 266 removed outlier: 3.695A pdb=" N VAL R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) Proline residue: R 229 - end of helix removed outlier: 4.464A pdb=" N ILE R 233 " --> pdb=" O PRO R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 288 removed outlier: 3.730A pdb=" N VAL R 273 " --> pdb=" O ASN R 269 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS R 274 " --> pdb=" O ALA R 270 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP R 275 " --> pdb=" O ALA R 271 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS R 279 " --> pdb=" O ASP R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 326 removed outlier: 3.750A pdb=" N ASP R 307 " --> pdb=" O PRO R 303 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE R 308 " --> pdb=" O GLU R 304 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG R 309 " --> pdb=" O MET R 305 " (cutoff:3.500A) Processing helix chain 'R' and resid 331 through 349 Processing helix chain 'R' and resid 365 through 392 removed outlier: 3.635A pdb=" N VAL R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N CYS R 380 " --> pdb=" O GLN R 376 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 403 through 424 removed outlier: 3.593A pdb=" N VAL R 407 " --> pdb=" O VAL R 403 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE R 415 " --> pdb=" O GLY R 411 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR R 416 " --> pdb=" O TYR R 412 " (cutoff:3.500A) Proline residue: R 419 - end of helix Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.813A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 206 removed outlier: 4.350A pdb=" N GLN H 206 " --> pdb=" O LEU H 203 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 Processing helix chain 'L' and resid 80 through 84 removed outlier: 4.105A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.668A pdb=" N ILE H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 14 through 15 removed outlier: 4.834A pdb=" N TYR H 116 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.014A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.014A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 164 through 168 removed outlier: 4.550A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 225 " --> pdb=" O TYR H 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.838A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA N 23 " --> pdb=" O GLN N 5 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU N 20 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.394A pdb=" N GLY N 10 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA N 33 " --> pdb=" O ASP N 98 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET N 34 " --> pdb=" O VAL N 50 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.669A pdb=" N LEU L 12 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR L 87 " --> pdb=" O THR L 104 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 90 through 92 removed outlier: 3.546A pdb=" N THR L 99 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.919A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 146 through 152 370 hydrogen bonds defined for protein. 1020 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: 2.97 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6670 1.04 - 1.23: 484 1.23 - 1.43: 2549 1.43 - 1.63: 3868 1.63 - 1.83: 48 Bond restraints: 13619 Sorted by residual: bond pdb=" ND2 ASN R 426 " pdb="HD21 ASN R 426 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN R 426 " pdb="HD22 ASN R 426 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" CA ASN R 426 " pdb=" C ASN R 426 " ideal model delta sigma weight residual 1.524 1.467 0.056 1.30e-02 5.92e+03 1.88e+01 bond pdb=" CA ASN R 426 " pdb=" CB ASN R 426 " ideal model delta sigma weight residual 1.528 1.490 0.039 1.66e-02 3.63e+03 5.40e+00 bond pdb=" C1 ZOB R 601 " pdb=" C2 ZOB R 601 " ideal model delta sigma weight residual 1.509 1.475 0.034 2.00e-02 2.50e+03 2.82e+00 ... (remaining 13614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.31: 24506 7.31 - 14.63: 3 14.63 - 21.94: 0 21.94 - 29.26: 1 29.26 - 36.57: 11 Bond angle restraints: 24521 Sorted by residual: angle pdb=" C ALA N 40 " pdb=" CA ALA N 40 " pdb=" HA ALA N 40 " ideal model delta sigma weight residual 109.00 72.43 36.57 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C GLN R 402 " pdb=" CA GLN R 402 " pdb=" HA GLN R 402 " ideal model delta sigma weight residual 109.00 73.73 35.27 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB LEU R 234 " pdb=" CA LEU R 234 " pdb=" HA LEU R 234 " ideal model delta sigma weight residual 109.00 73.76 35.24 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N GLN R 402 " pdb=" CA GLN R 402 " pdb=" HA GLN R 402 " ideal model delta sigma weight residual 110.00 74.91 35.09 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C CYS R 124 " pdb=" CA CYS R 124 " pdb=" HA CYS R 124 " ideal model delta sigma weight residual 109.00 74.13 34.87 3.00e+00 1.11e-01 1.35e+02 ... (remaining 24516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.45: 5973 18.45 - 36.91: 389 36.91 - 55.36: 112 55.36 - 73.81: 20 73.81 - 92.26: 6 Dihedral angle restraints: 6500 sinusoidal: 3451 harmonic: 3049 Sorted by residual: dihedral pdb=" CA ILE L 76 " pdb=" C ILE L 76 " pdb=" N SER L 77 " pdb=" CA SER L 77 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA GLU H 162 " pdb=" C GLU H 162 " pdb=" N PRO H 163 " pdb=" CA PRO H 163 " ideal model delta harmonic sigma weight residual 180.00 153.93 26.07 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN N 83 " pdb=" C ASN N 83 " pdb=" N SER N 84 " pdb=" CA SER N 84 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1004 0.090 - 0.179: 62 0.179 - 0.269: 1 0.269 - 0.358: 1 0.358 - 0.448: 3 Chirality restraints: 1071 Sorted by residual: chirality pdb=" CA GLN R 402 " pdb=" N GLN R 402 " pdb=" C GLN R 402 " pdb=" CB GLN R 402 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA ALA N 40 " pdb=" N ALA N 40 " pdb=" C ALA N 40 " pdb=" CB ALA N 40 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CA CYS R 124 " pdb=" N CYS R 124 " pdb=" C CYS R 124 " pdb=" CB CYS R 124 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 ... (remaining 1068 not shown) Planarity restraints: 2018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 426 " -0.053 2.00e-02 2.50e+03 5.11e-02 3.91e+01 pdb=" CG ASN R 426 " 0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN R 426 " 0.050 2.00e-02 2.50e+03 pdb=" ND2 ASN R 426 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN R 426 " 0.072 2.00e-02 2.50e+03 pdb="HD22 ASN R 426 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 382 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO R 383 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO R 383 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO R 383 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C27 ZOB R 601 " 0.022 2.00e-02 2.50e+03 1.22e-02 3.35e+00 pdb=" C28 ZOB R 601 " 0.002 2.00e-02 2.50e+03 pdb=" C29 ZOB R 601 " 0.000 2.00e-02 2.50e+03 pdb=" C30 ZOB R 601 " 0.007 2.00e-02 2.50e+03 pdb=" C32 ZOB R 601 " 0.000 2.00e-02 2.50e+03 pdb=" C33 ZOB R 601 " -0.002 2.00e-02 2.50e+03 pdb=" F34 ZOB R 601 " -0.017 2.00e-02 2.50e+03 pdb=" F35 ZOB R 601 " -0.021 2.00e-02 2.50e+03 pdb=" N31 ZOB R 601 " 0.008 2.00e-02 2.50e+03 ... (remaining 2015 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 282 2.13 - 2.75: 24146 2.75 - 3.36: 35759 3.36 - 3.98: 46155 3.98 - 4.60: 72519 Nonbonded interactions: 178861 Sorted by model distance: nonbonded pdb=" O TRP R 254 " pdb="HD21 ASN R 258 " model vdw 1.512 2.450 nonbonded pdb="HE22 GLN H 85 " pdb=" OD1 ASN H 87 " model vdw 1.561 2.450 nonbonded pdb="HD22 ASN R 69 " pdb=" OD2 ASP R 95 " model vdw 1.593 2.450 nonbonded pdb=" HA CYS R 124 " pdb=" HB3 CYS R 124 " model vdw 1.624 1.952 nonbonded pdb=" HA LEU R 234 " pdb=" HB2 LEU R 234 " model vdw 1.641 1.952 ... (remaining 178856 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.080 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6949 Z= 0.166 Angle : 0.616 10.387 9447 Z= 0.324 Chirality : 0.048 0.448 1071 Planarity : 0.004 0.052 1185 Dihedral : 13.647 92.264 2458 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.07 (0.30), residues: 859 helix: 1.93 (0.33), residues: 254 sheet: 0.25 (0.34), residues: 260 loop : -1.59 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 27 TYR 0.011 0.001 TYR L 92 PHE 0.013 0.001 PHE N 47 TRP 0.020 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 6943) covalent geometry : angle 0.61560 ( 9435) SS BOND : bond 0.00747 ( 6) SS BOND : angle 1.08978 ( 12) hydrogen bonds : bond 0.12398 ( 350) hydrogen bonds : angle 5.67198 ( 1020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 1.4339 time to fit residues: 202.4807 Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 85 GLN H 87 ASN L 102 GLN L 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.185377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137886 restraints weight = 21711.109| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.86 r_work: 0.3404 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6949 Z= 0.133 Angle : 0.589 10.543 9447 Z= 0.307 Chirality : 0.048 0.448 1071 Planarity : 0.004 0.051 1185 Dihedral : 6.875 73.724 971 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.91 % Allowed : 9.26 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.10 (0.30), residues: 859 helix: 1.91 (0.32), residues: 259 sheet: 0.22 (0.34), residues: 267 loop : -1.59 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 309 TYR 0.011 0.001 TYR L 92 PHE 0.015 0.001 PHE N 47 TRP 0.008 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 6943) covalent geometry : angle 0.58785 ( 9435) SS BOND : bond 0.00594 ( 6) SS BOND : angle 1.04227 ( 12) hydrogen bonds : bond 0.04441 ( 350) hydrogen bonds : angle 5.00477 ( 1020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7334 (tt) REVERT: H 22 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7973 (ttm-80) REVERT: H 226 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7199 (mm-30) REVERT: L 149 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (mp10) outliers start: 14 outliers final: 3 residues processed: 107 average time/residue: 1.3467 time to fit residues: 151.1710 Evaluate side-chains 102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 MET Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain L residue 149 GLN Chi-restraints excluded: chain L residue 160 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.182540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.134863 restraints weight = 21707.969| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.85 r_work: 0.3301 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6949 Z= 0.145 Angle : 0.580 10.640 9447 Z= 0.302 Chirality : 0.048 0.447 1071 Planarity : 0.004 0.051 1185 Dihedral : 6.454 61.036 971 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.63 % Allowed : 11.04 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.08 (0.29), residues: 859 helix: 1.94 (0.32), residues: 257 sheet: 0.19 (0.34), residues: 267 loop : -1.59 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 309 TYR 0.011 0.001 TYR L 92 PHE 0.018 0.001 PHE N 47 TRP 0.008 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6943) covalent geometry : angle 0.57866 ( 9435) SS BOND : bond 0.00581 ( 6) SS BOND : angle 1.21900 ( 12) hydrogen bonds : bond 0.04337 ( 350) hydrogen bonds : angle 4.84509 ( 1020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7300 (tt) REVERT: R 262 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6585 (ttmt) REVERT: H 22 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7989 (ttm-80) REVERT: L 82 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7540 (pm20) outliers start: 12 outliers final: 4 residues processed: 106 average time/residue: 1.3731 time to fit residues: 152.6782 Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 262 LYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 87 ASN L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.184194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147664 restraints weight = 21623.583| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.61 r_work: 0.3358 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6949 Z= 0.140 Angle : 0.571 10.640 9447 Z= 0.297 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.049 1185 Dihedral : 6.063 61.213 971 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.18 % Allowed : 11.31 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.14 (0.30), residues: 859 helix: 2.03 (0.32), residues: 257 sheet: 0.23 (0.34), residues: 269 loop : -1.63 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 72 TYR 0.011 0.001 TYR L 92 PHE 0.018 0.001 PHE N 47 TRP 0.009 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6943) covalent geometry : angle 0.56999 ( 9435) SS BOND : bond 0.00555 ( 6) SS BOND : angle 1.19762 ( 12) hydrogen bonds : bond 0.04203 ( 350) hydrogen bonds : angle 4.72409 ( 1020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7371 (tt) REVERT: R 286 ASP cc_start: 0.8610 (OUTLIER) cc_final: 0.8333 (t0) REVERT: H 22 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8038 (ttm-80) REVERT: L 82 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7571 (pm20) outliers start: 16 outliers final: 6 residues processed: 108 average time/residue: 1.3401 time to fit residues: 152.1019 Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.0060 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152623 restraints weight = 21717.848| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.43 r_work: 0.3368 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6949 Z= 0.109 Angle : 0.539 10.490 9447 Z= 0.280 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.049 1185 Dihedral : 5.513 61.258 971 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.50 % Allowed : 13.22 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.34 (0.30), residues: 859 helix: 2.24 (0.32), residues: 259 sheet: 0.32 (0.34), residues: 269 loop : -1.55 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 244 TYR 0.009 0.001 TYR L 92 PHE 0.014 0.001 PHE N 47 TRP 0.011 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6943) covalent geometry : angle 0.53800 ( 9435) SS BOND : bond 0.00484 ( 6) SS BOND : angle 1.09793 ( 12) hydrogen bonds : bond 0.03757 ( 350) hydrogen bonds : angle 4.55291 ( 1020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 163 MET cc_start: 0.7431 (tpp) cc_final: 0.7192 (tmm) REVERT: R 165 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7318 (tt) REVERT: H 22 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8008 (ttm-80) REVERT: L 189 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7996 (mm-30) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 1.3082 time to fit residues: 140.1684 Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 414 CYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148341 restraints weight = 21763.451| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.57 r_work: 0.3392 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6949 Z= 0.133 Angle : 0.557 10.657 9447 Z= 0.289 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.047 1185 Dihedral : 5.379 61.473 971 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.91 % Allowed : 13.49 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.26 (0.30), residues: 859 helix: 2.11 (0.32), residues: 261 sheet: 0.28 (0.34), residues: 269 loop : -1.55 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 45 TYR 0.011 0.001 TYR L 92 PHE 0.017 0.001 PHE N 47 TRP 0.015 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6943) covalent geometry : angle 0.55591 ( 9435) SS BOND : bond 0.00529 ( 6) SS BOND : angle 1.11492 ( 12) hydrogen bonds : bond 0.03951 ( 350) hydrogen bonds : angle 4.55552 ( 1020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7214 (tt) REVERT: R 226 PHE cc_start: 0.5393 (m-10) cc_final: 0.5081 (m-10) REVERT: R 244 ARG cc_start: 0.7879 (mmm-85) cc_final: 0.7583 (tpm-80) REVERT: R 286 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8351 (t0) REVERT: H 22 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7964 (ttm-80) REVERT: L 82 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: L 189 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8120 (mm-30) outliers start: 14 outliers final: 8 residues processed: 108 average time/residue: 1.2940 time to fit residues: 146.8041 Evaluate side-chains 107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 414 CYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 69 optimal weight: 0.0470 chunk 28 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN N 83 ASN L 102 GLN L 157 GLN L 191 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.185261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149720 restraints weight = 21776.380| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.50 r_work: 0.3384 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6949 Z= 0.112 Angle : 0.538 10.585 9447 Z= 0.278 Chirality : 0.047 0.444 1071 Planarity : 0.004 0.047 1185 Dihedral : 5.213 61.751 971 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.04 % Allowed : 14.31 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.37 (0.30), residues: 859 helix: 2.22 (0.32), residues: 261 sheet: 0.32 (0.34), residues: 269 loop : -1.49 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG N 45 TYR 0.010 0.001 TYR L 92 PHE 0.016 0.001 PHE N 47 TRP 0.014 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6943) covalent geometry : angle 0.53735 ( 9435) SS BOND : bond 0.00474 ( 6) SS BOND : angle 1.02486 ( 12) hydrogen bonds : bond 0.03690 ( 350) hydrogen bonds : angle 4.45952 ( 1020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7205 (tt) REVERT: R 226 PHE cc_start: 0.5417 (m-10) cc_final: 0.5075 (m-10) REVERT: R 244 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7651 (tpm-80) REVERT: R 286 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8343 (t0) REVERT: H 22 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7965 (ttm-80) REVERT: N 34 MET cc_start: 0.7649 (mmt) cc_final: 0.7398 (mmt) REVERT: L 82 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7391 (pm20) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 1.2819 time to fit residues: 140.0037 Evaluate side-chains 107 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain R residue 414 CYS Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN N 83 ASN L 102 GLN L 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.182215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135216 restraints weight = 21662.347| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.14 r_work: 0.3323 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6949 Z= 0.135 Angle : 0.559 10.653 9447 Z= 0.289 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.048 1185 Dihedral : 5.276 61.941 971 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.45 % Allowed : 14.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.27 (0.30), residues: 859 helix: 2.13 (0.32), residues: 261 sheet: 0.28 (0.34), residues: 269 loop : -1.55 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 45 TYR 0.011 0.001 TYR L 92 PHE 0.017 0.001 PHE N 47 TRP 0.017 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 6943) covalent geometry : angle 0.55809 ( 9435) SS BOND : bond 0.00522 ( 6) SS BOND : angle 1.11565 ( 12) hydrogen bonds : bond 0.03883 ( 350) hydrogen bonds : angle 4.49234 ( 1020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7208 (tt) REVERT: R 226 PHE cc_start: 0.5622 (m-10) cc_final: 0.5194 (m-10) REVERT: R 286 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8325 (t0) REVERT: H 22 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7921 (ttm-80) REVERT: N 34 MET cc_start: 0.7617 (mmt) cc_final: 0.7394 (mmt) REVERT: L 82 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7345 (pm20) outliers start: 18 outliers final: 5 residues processed: 103 average time/residue: 1.3152 time to fit residues: 142.2911 Evaluate side-chains 101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN N 83 ASN L 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147862 restraints weight = 21825.354| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.61 r_work: 0.3362 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 6949 Z= 0.147 Angle : 0.595 11.592 9447 Z= 0.306 Chirality : 0.048 0.443 1071 Planarity : 0.004 0.048 1185 Dihedral : 5.374 62.082 971 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.63 % Allowed : 15.40 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: 0.25 (0.30), residues: 859 helix: 2.12 (0.32), residues: 261 sheet: 0.26 (0.34), residues: 269 loop : -1.56 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 45 TYR 0.010 0.001 TYR H 98 PHE 0.017 0.001 PHE N 47 TRP 0.018 0.002 TRP R 176 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6943) covalent geometry : angle 0.58094 ( 9435) SS BOND : bond 0.00437 ( 6) SS BOND : angle 3.64341 ( 12) hydrogen bonds : bond 0.04043 ( 350) hydrogen bonds : angle 4.59571 ( 1020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 104 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7242 (tt) REVERT: R 226 PHE cc_start: 0.5658 (m-10) cc_final: 0.5227 (m-10) REVERT: R 244 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7633 (tpm-80) REVERT: R 286 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8362 (t0) REVERT: H 22 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7977 (ttm-80) REVERT: N 34 MET cc_start: 0.7669 (mmt) cc_final: 0.7460 (mmt) REVERT: L 82 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7408 (pm20) outliers start: 12 outliers final: 6 residues processed: 99 average time/residue: 1.4038 time to fit residues: 145.7024 Evaluate side-chains 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain L residue 211 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN N 83 ASN L 102 GLN L 157 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.181566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133902 restraints weight = 21889.438| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.84 r_work: 0.3387 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6949 Z= 0.140 Angle : 0.583 10.625 9447 Z= 0.301 Chirality : 0.048 0.442 1071 Planarity : 0.004 0.051 1185 Dihedral : 5.346 62.452 971 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.77 % Allowed : 15.53 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.27 (0.30), residues: 859 helix: 2.04 (0.32), residues: 264 sheet: 0.31 (0.34), residues: 267 loop : -1.53 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 45 TYR 0.010 0.001 TYR L 92 PHE 0.018 0.001 PHE N 47 TRP 0.022 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 6943) covalent geometry : angle 0.57498 ( 9435) SS BOND : bond 0.00545 ( 6) SS BOND : angle 2.79585 ( 12) hydrogen bonds : bond 0.04010 ( 350) hydrogen bonds : angle 4.56831 ( 1020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1718 Ramachandran restraints generated. 859 Oldfield, 0 Emsley, 859 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 362 is missing expected H atoms. Skipping. Residue VAL 364 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue LYS 40 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7240 (tt) REVERT: R 226 PHE cc_start: 0.5474 (m-10) cc_final: 0.5048 (m-10) REVERT: R 244 ARG cc_start: 0.7877 (mmm-85) cc_final: 0.7578 (tpm-80) REVERT: R 286 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8320 (t0) REVERT: H 22 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7911 (ttm-80) REVERT: N 34 MET cc_start: 0.7562 (mmt) cc_final: 0.7350 (mmt) REVERT: L 82 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7310 (pm20) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 1.2957 time to fit residues: 135.9535 Evaluate side-chains 102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 286 ASP Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 22 ARG Chi-restraints excluded: chain H residue 170 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 73 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN L 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.184946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137827 restraints weight = 22007.545| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 1.85 r_work: 0.3407 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6949 Z= 0.116 Angle : 0.562 10.506 9447 Z= 0.289 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.050 1185 Dihedral : 5.245 62.824 971 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.36 % Allowed : 16.49 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 0.43 (0.30), residues: 859 helix: 1.97 (0.32), residues: 271 sheet: 0.40 (0.34), residues: 267 loop : -1.31 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 244 TYR 0.009 0.001 TYR L 92 PHE 0.022 0.001 PHE L 211 TRP 0.022 0.001 TRP R 176 HIS 0.002 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6943) covalent geometry : angle 0.55560 ( 9435) SS BOND : bond 0.00484 ( 6) SS BOND : angle 2.43341 ( 12) hydrogen bonds : bond 0.03671 ( 350) hydrogen bonds : angle 4.46983 ( 1020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5773.01 seconds wall clock time: 98 minutes 16.63 seconds (5896.63 seconds total)