Starting phenix.real_space_refine on Thu Jun 12 21:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tb7_41145/06_2025/8tb7_41145_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tb7_41145/06_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_41145/06_2025/8tb7_41145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tb7_41145/06_2025/8tb7_41145.map" model { file = "/net/cci-nas-00/data/ceres_data/8tb7_41145/06_2025/8tb7_41145_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tb7_41145/06_2025/8tb7_41145_trim.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.35, per 1000 atoms: 0.47 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: 3.24 Conformation dependent library (CDL) restraints added in 999.7 milliseconds 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: 1.27 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: 4.70 Time building geometry restraints manager: 3.99 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.130 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- 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 : 5.57 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (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 TRP 0.020 0.001 TRP N 110 HIS 0.004 0.001 HIS L 200 PHE 0.013 0.001 PHE N 47 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG N 27 Details of bonding type rmsd hydrogen bonds : bond 0.12398 ( 350) hydrogen bonds : angle 5.67198 ( 1020) SS BOND : bond 0.00747 ( 6) SS BOND : angle 1.08978 ( 12) covalent geometry : bond 0.00353 ( 6943) covalent geometry : angle 0.61560 ( 9435) *********************** 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 : 1.008 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: 2.6073 time to fit residues: 369.9272 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 : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4071 r_free = 0.4071 target = 0.184678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137221 restraints weight = 21569.123| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.84 r_work: 0.3332 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6949 Z= 0.147 Angle : 0.598 10.547 9447 Z= 0.312 Chirality : 0.048 0.447 1071 Planarity : 0.004 0.051 1185 Dihedral : 6.897 73.443 971 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.04 % Allowed : 8.99 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.29), residues: 859 helix: 1.87 (0.32), residues: 259 sheet: 0.18 (0.33), residues: 267 loop : -1.62 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 PHE 0.016 0.001 PHE N 47 TYR 0.012 0.001 TYR L 92 ARG 0.002 0.000 ARG R 309 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 350) hydrogen bonds : angle 5.01038 ( 1020) SS BOND : bond 0.00615 ( 6) SS BOND : angle 1.10439 ( 12) covalent geometry : bond 0.00343 ( 6943) covalent geometry : angle 0.59740 ( 9435) *********************** 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 116 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7309 (tt) REVERT: H 22 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7991 (ttm-80) REVERT: L 149 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7908 (mp10) outliers start: 15 outliers final: 3 residues processed: 109 average time/residue: 2.4638 time to fit residues: 283.2433 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 : 1.022 ------------------------------------------------------------------------------- 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 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.182599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134199 restraints weight = 21691.742| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.90 r_work: 0.3420 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6949 Z= 0.140 Angle : 0.577 10.654 9447 Z= 0.300 Chirality : 0.048 0.447 1071 Planarity : 0.004 0.051 1185 Dihedral : 6.422 61.104 971 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.63 % Allowed : 10.90 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.30), residues: 859 helix: 1.97 (0.32), residues: 257 sheet: 0.19 (0.34), residues: 267 loop : -1.61 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 176 HIS 0.004 0.001 HIS L 200 PHE 0.017 0.001 PHE N 47 TYR 0.011 0.001 TYR L 92 ARG 0.002 0.000 ARG R 309 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 350) hydrogen bonds : angle 4.83200 ( 1020) SS BOND : bond 0.00570 ( 6) SS BOND : angle 1.19100 ( 12) covalent geometry : bond 0.00328 ( 6943) covalent geometry : angle 0.57563 ( 9435) *********************** 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 111 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7315 (tt) REVERT: R 262 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6563 (ttmt) REVERT: H 22 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: H 226 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7411 (mm-30) REVERT: L 82 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7543 (pm20) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 2.4096 time to fit residues: 267.1469 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 : 1.019 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 45 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.185711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.150298 restraints weight = 21564.945| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.57 r_work: 0.3357 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6949 Z= 0.112 Angle : 0.547 10.502 9447 Z= 0.284 Chirality : 0.047 0.447 1071 Planarity : 0.004 0.048 1185 Dihedral : 5.873 61.105 971 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.63 % Allowed : 12.13 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 859 helix: 2.18 (0.32), residues: 257 sheet: 0.26 (0.34), residues: 267 loop : -1.55 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.014 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 350) hydrogen bonds : angle 4.63763 ( 1020) SS BOND : bond 0.00503 ( 6) SS BOND : angle 1.10363 ( 12) covalent geometry : bond 0.00256 ( 6943) covalent geometry : angle 0.54601 ( 9435) *********************** 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 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7367 (tt) REVERT: R 226 PHE cc_start: 0.5534 (m-10) cc_final: 0.5190 (m-10) REVERT: H 22 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8044 (ttm-80) REVERT: H 226 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7444 (mm-30) outliers start: 12 outliers final: 4 residues processed: 105 average time/residue: 2.3753 time to fit residues: 263.6671 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 : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 410 ILE Chi-restraints excluded: chain H residue 22 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.182346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.134427 restraints weight = 21864.291| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.85 r_work: 0.3363 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6949 Z= 0.180 Angle : 0.607 10.830 9447 Z= 0.316 Chirality : 0.048 0.445 1071 Planarity : 0.005 0.050 1185 Dihedral : 5.796 61.439 971 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.32 % Allowed : 12.53 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 859 helix: 1.86 (0.31), residues: 263 sheet: 0.13 (0.33), residues: 269 loop : -1.70 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 110 HIS 0.005 0.001 HIS L 200 PHE 0.021 0.002 PHE N 47 TYR 0.013 0.002 TYR L 92 ARG 0.002 0.000 ARG R 309 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 350) hydrogen bonds : angle 4.76744 ( 1020) SS BOND : bond 0.00617 ( 6) SS BOND : angle 1.34128 ( 12) covalent geometry : bond 0.00428 ( 6943) covalent geometry : angle 0.60522 ( 9435) *********************** 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 119 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7286 (tt) REVERT: R 226 PHE cc_start: 0.5560 (m-10) cc_final: 0.5147 (m-10) REVERT: R 286 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8257 (t0) REVERT: H 22 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7901 (ttm-80) REVERT: H 162 GLU cc_start: 0.8003 (tt0) cc_final: 0.7697 (tt0) REVERT: H 226 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7424 (mm-30) REVERT: L 82 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7387 (pm20) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 2.7254 time to fit residues: 325.7831 Evaluate side-chains 111 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 163 GLU 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 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 0.0970 chunk 67 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 L 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.148566 restraints weight = 21901.540| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.58 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6949 Z= 0.114 Angle : 0.549 10.527 9447 Z= 0.284 Chirality : 0.047 0.442 1071 Planarity : 0.004 0.049 1185 Dihedral : 5.411 61.378 971 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.04 % Allowed : 13.90 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.30), residues: 859 helix: 2.10 (0.32), residues: 261 sheet: 0.20 (0.34), residues: 269 loop : -1.57 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.015 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.03845 ( 350) hydrogen bonds : angle 4.56071 ( 1020) SS BOND : bond 0.00500 ( 6) SS BOND : angle 1.10217 ( 12) covalent geometry : bond 0.00265 ( 6943) covalent geometry : angle 0.54797 ( 9435) *********************** 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 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7239 (tt) REVERT: R 226 PHE cc_start: 0.5531 (m-10) cc_final: 0.5067 (m-10) REVERT: R 244 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7619 (tpm-80) REVERT: H 22 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7951 (ttm-80) REVERT: H 226 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7371 (mm-30) REVERT: L 82 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7381 (pm20) outliers start: 15 outliers final: 7 residues processed: 107 average time/residue: 2.2964 time to fit residues: 260.0859 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 : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU 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 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 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 L 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.148167 restraints weight = 21816.740| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.61 r_work: 0.3367 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6949 Z= 0.131 Angle : 0.579 12.066 9447 Z= 0.299 Chirality : 0.048 0.442 1071 Planarity : 0.004 0.052 1185 Dihedral : 5.411 62.002 971 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.77 % Allowed : 15.40 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.30), residues: 859 helix: 2.15 (0.32), residues: 261 sheet: 0.21 (0.34), residues: 269 loop : -1.56 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.016 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.04033 ( 350) hydrogen bonds : angle 4.61827 ( 1020) SS BOND : bond 0.00412 ( 6) SS BOND : angle 3.67373 ( 12) covalent geometry : bond 0.00315 ( 6943) covalent geometry : angle 0.56473 ( 9435) *********************** 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 112 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7222 (tt) REVERT: R 226 PHE cc_start: 0.5613 (m-10) cc_final: 0.5129 (m-10) REVERT: R 286 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8351 (t0) REVERT: R 410 ILE cc_start: 0.6538 (OUTLIER) cc_final: 0.6336 (mp) REVERT: H 22 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7951 (ttm-80) REVERT: H 226 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7363 (mm-30) REVERT: N 34 MET cc_start: 0.7676 (mmt) cc_final: 0.7451 (mmt) REVERT: L 82 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7394 (pm20) REVERT: L 149 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7692 (mp10) outliers start: 13 outliers final: 5 residues processed: 105 average time/residue: 2.5259 time to fit residues: 280.2979 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 : 0.930 ------------------------------------------------------------------------------- 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 149 GLN 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 4 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 L 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.182262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145577 restraints weight = 21836.447| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.66 r_work: 0.3385 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6949 Z= 0.129 Angle : 0.572 11.057 9447 Z= 0.296 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.054 1185 Dihedral : 5.361 62.094 971 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.32 % Allowed : 15.12 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 859 helix: 2.14 (0.32), residues: 261 sheet: 0.30 (0.34), residues: 267 loop : -1.59 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 110 HIS 0.003 0.001 HIS L 200 PHE 0.016 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.003 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 350) hydrogen bonds : angle 4.57870 ( 1020) SS BOND : bond 0.00516 ( 6) SS BOND : angle 3.32970 ( 12) covalent geometry : bond 0.00310 ( 6943) covalent geometry : angle 0.56039 ( 9435) *********************** 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 113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7196 (tt) REVERT: R 226 PHE cc_start: 0.5645 (m-10) cc_final: 0.5136 (m-10) REVERT: R 244 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7580 (tpm-80) REVERT: R 286 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8332 (t0) REVERT: H 22 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7940 (ttm-80) REVERT: H 226 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7353 (mm-30) REVERT: N 34 MET cc_start: 0.7639 (mmt) cc_final: 0.7419 (mmt) REVERT: L 82 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7384 (pm20) outliers start: 17 outliers final: 6 residues processed: 104 average time/residue: 2.5577 time to fit residues: 280.8150 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 : 1.055 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.182417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.145837 restraints weight = 21672.113| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.60 r_work: 0.3366 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6949 Z= 0.131 Angle : 0.573 10.571 9447 Z= 0.296 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.054 1185 Dihedral : 5.336 62.314 971 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.36 % Allowed : 15.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 859 helix: 2.11 (0.32), residues: 262 sheet: 0.34 (0.34), residues: 265 loop : -1.55 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 176 HIS 0.003 0.001 HIS L 200 PHE 0.016 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 350) hydrogen bonds : angle 4.56504 ( 1020) SS BOND : bond 0.00517 ( 6) SS BOND : angle 3.01498 ( 12) covalent geometry : bond 0.00313 ( 6943) covalent geometry : angle 0.56299 ( 9435) *********************** 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 103 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7230 (tt) REVERT: R 226 PHE cc_start: 0.5636 (m-10) cc_final: 0.5104 (m-10) REVERT: R 244 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7622 (tpm-80) REVERT: H 22 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7942 (ttm-80) REVERT: H 226 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7339 (mm-30) REVERT: N 34 MET cc_start: 0.7625 (mmt) cc_final: 0.7411 (mmt) REVERT: L 82 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7378 (pm20) outliers start: 10 outliers final: 5 residues processed: 98 average time/residue: 2.5766 time to fit residues: 266.3606 Evaluate side-chains 101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU 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 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 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 L 157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.181232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.132876 restraints weight = 21764.754| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.90 r_work: 0.3330 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6949 Z= 0.155 Angle : 0.596 10.720 9447 Z= 0.308 Chirality : 0.048 0.442 1071 Planarity : 0.004 0.053 1185 Dihedral : 5.417 62.389 971 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.23 % Allowed : 16.21 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 859 helix: 2.01 (0.32), residues: 264 sheet: 0.27 (0.34), residues: 265 loop : -1.60 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 176 HIS 0.004 0.001 HIS L 200 PHE 0.019 0.001 PHE N 47 TYR 0.011 0.001 TYR H 98 ARG 0.003 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 350) hydrogen bonds : angle 4.63992 ( 1020) SS BOND : bond 0.00545 ( 6) SS BOND : angle 2.95563 ( 12) covalent geometry : bond 0.00375 ( 6943) covalent geometry : angle 0.58677 ( 9435) ********************** 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 101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 165 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7222 (tt) REVERT: R 226 PHE cc_start: 0.5718 (m-10) cc_final: 0.5177 (m-10) REVERT: R 244 ARG cc_start: 0.7760 (mmm-85) cc_final: 0.7455 (tpm-80) REVERT: H 22 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7880 (ttm-80) REVERT: H 226 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7334 (mm-30) REVERT: L 82 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7345 (pm20) outliers start: 9 outliers final: 4 residues processed: 97 average time/residue: 2.6016 time to fit residues: 265.6329 Evaluate side-chains 98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 165 LEU 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 82 GLU 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 71 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.0370 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.182753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.134613 restraints weight = 21827.080| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.90 r_work: 0.3339 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6949 Z= 0.120 Angle : 0.564 10.486 9447 Z= 0.291 Chirality : 0.047 0.443 1071 Planarity : 0.004 0.053 1185 Dihedral : 5.290 62.654 971 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.95 % Allowed : 16.76 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.30), residues: 859 helix: 2.01 (0.32), residues: 270 sheet: 0.33 (0.34), residues: 265 loop : -1.44 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 176 HIS 0.002 0.001 HIS L 200 PHE 0.015 0.001 PHE N 47 TYR 0.010 0.001 TYR L 92 ARG 0.002 0.000 ARG N 45 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 350) hydrogen bonds : angle 4.52293 ( 1020) SS BOND : bond 0.00516 ( 6) SS BOND : angle 2.76885 ( 12) covalent geometry : bond 0.00287 ( 6943) covalent geometry : angle 0.55545 ( 9435) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11035.71 seconds wall clock time: 190 minutes 35.17 seconds (11435.17 seconds total)