Starting phenix.real_space_refine on Fri Aug 22 17:07:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4e_39762/08_2025/8z4e_39762.map" } resolution = 3.0 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= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 39 5.16 5 C 3979 2.51 5 N 1074 2.21 5 O 1234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6327 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2631 Classifications: {'peptide': 339} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 316} Chain breaks: 3 Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 811 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 105} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 988 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "E" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1024 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "F" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.37, per 1000 atoms: 0.22 Number of scatterers: 6327 At special positions: 0 Unit cell: (68.88, 97.58, 123.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 39 16.00 O 1234 8.00 N 1074 7.00 C 3979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.04 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 449 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 201 " Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 224.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 16 sheets defined 2.8% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'C' and resid 87 through 91 removed outlier: 4.007A pdb=" N THR C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.621A pdb=" N ASP E 31 " --> pdb=" O LYS E 28 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.670A pdb=" N LYS E 64 " --> pdb=" O ASP E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 125 removed outlier: 5.499A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N CYS A 176 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N SER A 160 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 180 through 185 removed outlier: 4.102A pdb=" N SER A 180 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ALA A 204 " --> pdb=" O GLU A 215 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 215 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 206 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 211 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 244 removed outlier: 3.880A pdb=" N LYS A 265 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS A 259 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.932A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 292 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 357 removed outlier: 5.896A pdb=" N SER A 373 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ASN A 400 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N MET A 377 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU A 396 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 407 through 411 Processing sheet with id=AA7, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.560A pdb=" N LEU B 48 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 50 removed outlier: 5.560A pdb=" N LEU B 48 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN B 39 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12 removed outlier: 8.315A pdb=" N TYR C 32 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE C 52 " --> pdb=" O TYR C 32 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.558A pdb=" N VAL E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 57 through 59 removed outlier: 3.558A pdb=" N VAL E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.976A pdb=" N ILE F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.021A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 567 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: 1.02 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2030 1.34 - 1.46: 1672 1.46 - 1.59: 2730 1.59 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 6484 Sorted by residual: bond pdb=" C THR A 392 " pdb=" N SER A 393 " ideal model delta sigma weight residual 1.332 1.297 0.035 1.40e-02 5.10e+03 6.30e+00 bond pdb=" N THR A 392 " pdb=" CA THR A 392 " ideal model delta sigma weight residual 1.458 1.473 -0.015 6.30e-03 2.52e+04 5.42e+00 bond pdb=" CA SER A 393 " pdb=" CB SER A 393 " ideal model delta sigma weight residual 1.530 1.499 0.032 1.69e-02 3.50e+03 3.50e+00 bond pdb=" N SER A 393 " pdb=" CA SER A 393 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.60e+00 bond pdb=" C PRO A 391 " pdb=" O PRO A 391 " ideal model delta sigma weight residual 1.234 1.217 0.017 1.14e-02 7.69e+03 2.21e+00 ... (remaining 6479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 8547 1.56 - 3.13: 229 3.13 - 4.69: 24 4.69 - 6.25: 6 6.25 - 7.81: 3 Bond angle restraints: 8809 Sorted by residual: angle pdb=" C PRO A 391 " pdb=" CA PRO A 391 " pdb=" CB PRO A 391 " ideal model delta sigma weight residual 110.98 103.17 7.81 1.31e+00 5.83e-01 3.56e+01 angle pdb=" C THR A 392 " pdb=" CA THR A 392 " pdb=" CB THR A 392 " ideal model delta sigma weight residual 116.54 123.52 -6.98 1.46e+00 4.69e-01 2.29e+01 angle pdb=" C SER A 393 " pdb=" N TYR A 394 " pdb=" CA TYR A 394 " ideal model delta sigma weight residual 122.65 128.41 -5.76 1.49e+00 4.50e-01 1.49e+01 angle pdb=" N LEU A 100 " pdb=" CA LEU A 100 " pdb=" C LEU A 100 " ideal model delta sigma weight residual 114.04 109.26 4.78 1.24e+00 6.50e-01 1.48e+01 angle pdb=" N PRO A 391 " pdb=" CA PRO A 391 " pdb=" C PRO A 391 " ideal model delta sigma weight residual 111.38 117.17 -5.79 1.59e+00 3.96e-01 1.33e+01 ... (remaining 8804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3537 17.43 - 34.86: 262 34.86 - 52.30: 51 52.30 - 69.73: 11 69.73 - 87.16: 3 Dihedral angle restraints: 3864 sinusoidal: 1529 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS A 292 " pdb=" CB CYS A 292 " ideal model delta sinusoidal sigma weight residual 93.00 42.05 50.95 1 1.00e+01 1.00e-02 3.55e+01 dihedral pdb=" CB CYS A 423 " pdb=" SG CYS A 423 " pdb=" SG CYS A 449 " pdb=" CB CYS A 449 " ideal model delta sinusoidal sigma weight residual 93.00 52.33 40.67 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" C THR A 392 " pdb=" N THR A 392 " pdb=" CA THR A 392 " pdb=" CB THR A 392 " ideal model delta harmonic sigma weight residual -122.00 -133.80 11.80 0 2.50e+00 1.60e-01 2.23e+01 ... (remaining 3861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 812 0.062 - 0.125: 132 0.125 - 0.187: 7 0.187 - 0.250: 0 0.250 - 0.312: 2 Chirality restraints: 953 Sorted by residual: chirality pdb=" CA SER A 393 " pdb=" N SER A 393 " pdb=" C SER A 393 " pdb=" CB SER A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA THR A 392 " pdb=" N THR A 392 " pdb=" C THR A 392 " pdb=" CB THR A 392 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 201 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 950 not shown) Planarity restraints: 1131 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 39 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.46e+00 pdb=" N PRO F 40 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 40 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 40 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 168 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 169 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 169 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 169 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C THR A 392 " -0.032 2.00e-02 2.50e+03 pdb=" O THR A 392 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 393 " 0.011 2.00e-02 2.50e+03 ... (remaining 1128 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 898 2.76 - 3.30: 5579 3.30 - 3.83: 10393 3.83 - 4.37: 11891 4.37 - 4.90: 21360 Nonbonded interactions: 50121 Sorted by model distance: nonbonded pdb=" OG SER B 11 " pdb=" O THR B 108 " model vdw 2.230 3.040 nonbonded pdb=" OH TYR B 32 " pdb=" OG SER B 95 " model vdw 2.238 3.040 nonbonded pdb=" OG SER A 229 " pdb=" O CYS A 279 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR B 93 " pdb=" O SER C 111 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR A 387 " pdb=" OE1 GLN A 388 " model vdw 2.274 3.040 ... (remaining 50116 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 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 : 0.003 0.035 6498 Z= 0.146 Angle : 0.616 7.815 8839 Z= 0.346 Chirality : 0.046 0.312 953 Planarity : 0.005 0.064 1130 Dihedral : 12.618 87.159 2346 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.09 % Favored : 93.42 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.63 (0.30), residues: 805 helix: -1.48 (2.33), residues: 6 sheet: 1.09 (0.30), residues: 313 loop : -1.55 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 454 TYR 0.008 0.001 TYR F 86 PHE 0.008 0.001 PHE A 132 TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6484) covalent geometry : angle 0.61108 ( 8809) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.62686 ( 24) hydrogen bonds : bond 0.09536 ( 201) hydrogen bonds : angle 6.94040 ( 567) link_BETA1-4 : bond 0.00218 ( 1) link_BETA1-4 : angle 1.34418 ( 3) link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 0.42911 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.182 Fit side-chains REVERT: A 155 PHE cc_start: 0.6327 (p90) cc_final: 0.4792 (p90) REVERT: A 327 SER cc_start: 0.7944 (p) cc_final: 0.7675 (t) REVERT: A 357 ASP cc_start: 0.7460 (t0) cc_final: 0.7096 (t0) REVERT: C 43 GLN cc_start: 0.7104 (mp10) cc_final: 0.6421 (mp10) REVERT: C 98 ARG cc_start: 0.6896 (ttp-170) cc_final: 0.6657 (ttp-170) REVERT: E 83 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7753 (mtmt) REVERT: F 9 SER cc_start: 0.7361 (m) cc_final: 0.7000 (p) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.4165 time to fit residues: 45.2855 Evaluate side-chains 95 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN B 40 GLN C 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.159916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146092 restraints weight = 9355.985| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.58 r_work: 0.3858 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6498 Z= 0.231 Angle : 0.660 7.183 8839 Z= 0.340 Chirality : 0.047 0.166 953 Planarity : 0.006 0.055 1130 Dihedral : 4.851 29.932 931 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.33 % Favored : 92.17 % Rotamer: Outliers : 1.89 % Allowed : 9.14 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.71 (0.29), residues: 805 helix: -1.99 (1.98), residues: 6 sheet: 1.13 (0.30), residues: 312 loop : -1.67 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 18 TYR 0.023 0.002 TYR C 114 PHE 0.016 0.002 PHE F 98 TRP 0.014 0.002 TRP A 207 HIS 0.007 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 6484) covalent geometry : angle 0.65610 ( 8809) SS BOND : bond 0.00546 ( 12) SS BOND : angle 1.46660 ( 24) hydrogen bonds : bond 0.03526 ( 201) hydrogen bonds : angle 6.13313 ( 567) link_BETA1-4 : bond 0.00444 ( 1) link_BETA1-4 : angle 0.66184 ( 3) link_NAG-ASN : bond 0.00102 ( 1) link_NAG-ASN : angle 0.46199 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7874 (p) cc_final: 0.7445 (m) REVERT: A 209 ARG cc_start: 0.7613 (mtp-110) cc_final: 0.7388 (mtp180) REVERT: A 211 ARG cc_start: 0.7231 (ptt-90) cc_final: 0.6943 (ptt-90) REVERT: A 327 SER cc_start: 0.8232 (p) cc_final: 0.7990 (t) REVERT: A 353 PHE cc_start: 0.8153 (p90) cc_final: 0.7795 (p90) REVERT: A 426 VAL cc_start: 0.6764 (t) cc_final: 0.6510 (p) REVERT: B 112 GLN cc_start: 0.7239 (pp30) cc_final: 0.6938 (pp30) REVERT: C 6 GLN cc_start: 0.8184 (mt0) cc_final: 0.7947 (mt0) REVERT: C 98 ARG cc_start: 0.7485 (ttp-170) cc_final: 0.7151 (ttp-170) REVERT: E 83 LYS cc_start: 0.8294 (mtmt) cc_final: 0.8049 (mtmt) outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 0.3816 time to fit residues: 43.5074 Evaluate side-chains 105 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 445 MET Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 108 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.160656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.146820 restraints weight = 9171.668| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.54 r_work: 0.3869 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6498 Z= 0.149 Angle : 0.578 6.661 8839 Z= 0.297 Chirality : 0.044 0.150 953 Planarity : 0.005 0.062 1130 Dihedral : 4.511 20.348 931 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.34 % Favored : 94.16 % Rotamer: Outliers : 2.61 % Allowed : 13.35 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.60 (0.30), residues: 805 helix: -1.92 (2.04), residues: 6 sheet: 1.15 (0.29), residues: 322 loop : -1.61 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 18 TYR 0.022 0.002 TYR A 375 PHE 0.010 0.001 PHE F 98 TRP 0.009 0.001 TRP A 207 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6484) covalent geometry : angle 0.57594 ( 8809) SS BOND : bond 0.00343 ( 12) SS BOND : angle 1.18537 ( 24) hydrogen bonds : bond 0.03049 ( 201) hydrogen bonds : angle 5.86543 ( 567) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 0.79520 ( 3) link_NAG-ASN : bond 0.00030 ( 1) link_NAG-ASN : angle 0.38931 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.223 Fit side-chains REVERT: A 94 VAL cc_start: 0.7884 (p) cc_final: 0.7436 (m) REVERT: A 293 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.6682 (ptp-170) REVERT: A 310 MET cc_start: 0.6344 (mmp) cc_final: 0.6135 (mmp) REVERT: A 315 SER cc_start: 0.8688 (m) cc_final: 0.8252 (t) REVERT: A 324 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7772 (p) REVERT: A 327 SER cc_start: 0.8219 (p) cc_final: 0.7990 (t) REVERT: A 353 PHE cc_start: 0.8143 (p90) cc_final: 0.7707 (p90) REVERT: A 357 ASP cc_start: 0.7876 (t0) cc_final: 0.7430 (t0) REVERT: B 112 GLN cc_start: 0.7146 (pp30) cc_final: 0.6837 (pp30) REVERT: C 6 GLN cc_start: 0.8192 (mt0) cc_final: 0.7970 (mt0) REVERT: C 43 GLN cc_start: 0.7349 (mp10) cc_final: 0.6602 (mp10) REVERT: C 48 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6527 (ttp) REVERT: C 98 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.7155 (ttp-170) REVERT: E 83 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8012 (mtmt) REVERT: F 17 ASP cc_start: 0.7188 (m-30) cc_final: 0.6985 (m-30) outliers start: 18 outliers final: 8 residues processed: 105 average time/residue: 0.3899 time to fit residues: 43.5441 Evaluate side-chains 110 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 108 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.159979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.146176 restraints weight = 9272.832| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.56 r_work: 0.3853 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6498 Z= 0.170 Angle : 0.589 6.521 8839 Z= 0.301 Chirality : 0.045 0.156 953 Planarity : 0.005 0.052 1130 Dihedral : 4.568 19.186 931 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.08 % Favored : 92.42 % Rotamer: Outliers : 2.76 % Allowed : 14.22 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.63 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 1.02 (0.29), residues: 330 loop : -1.59 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 18 TYR 0.021 0.002 TYR C 114 PHE 0.012 0.001 PHE F 98 TRP 0.010 0.001 TRP B 37 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6484) covalent geometry : angle 0.58582 ( 8809) SS BOND : bond 0.00335 ( 12) SS BOND : angle 1.31642 ( 24) hydrogen bonds : bond 0.03064 ( 201) hydrogen bonds : angle 5.81881 ( 567) link_BETA1-4 : bond 0.00157 ( 1) link_BETA1-4 : angle 0.79898 ( 3) link_NAG-ASN : bond 0.00092 ( 1) link_NAG-ASN : angle 0.45847 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.144 Fit side-chains REVERT: A 94 VAL cc_start: 0.7937 (p) cc_final: 0.7491 (m) REVERT: A 191 MET cc_start: 0.7756 (ttp) cc_final: 0.7258 (ttp) REVERT: A 293 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.6616 (ptp-170) REVERT: A 324 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7759 (p) REVERT: A 327 SER cc_start: 0.8231 (p) cc_final: 0.8007 (t) REVERT: A 353 PHE cc_start: 0.8231 (p90) cc_final: 0.7667 (p90) REVERT: A 357 ASP cc_start: 0.7857 (t0) cc_final: 0.7398 (t0) REVERT: B 112 GLN cc_start: 0.7240 (pp30) cc_final: 0.6986 (pp30) REVERT: C 43 GLN cc_start: 0.7359 (mp10) cc_final: 0.6608 (mp10) REVERT: C 48 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6599 (mtp) REVERT: C 98 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7166 (ttp-170) REVERT: E 83 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8038 (mtmt) outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 0.3867 time to fit residues: 43.9723 Evaluate side-chains 109 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 6 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 6 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.159183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.145347 restraints weight = 9341.671| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.55 r_work: 0.3834 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6498 Z= 0.166 Angle : 0.598 6.470 8839 Z= 0.305 Chirality : 0.045 0.157 953 Planarity : 0.005 0.049 1130 Dihedral : 4.563 17.943 931 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.46 % Favored : 93.04 % Rotamer: Outliers : 3.19 % Allowed : 15.38 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.61 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 1.04 (0.29), residues: 329 loop : -1.58 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 18 TYR 0.021 0.002 TYR A 375 PHE 0.013 0.001 PHE F 98 TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 6484) covalent geometry : angle 0.59149 ( 8809) SS BOND : bond 0.00358 ( 12) SS BOND : angle 1.78159 ( 24) hydrogen bonds : bond 0.03037 ( 201) hydrogen bonds : angle 5.79706 ( 567) link_BETA1-4 : bond 0.00138 ( 1) link_BETA1-4 : angle 0.83077 ( 3) link_NAG-ASN : bond 0.00105 ( 1) link_NAG-ASN : angle 0.46749 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: A 94 VAL cc_start: 0.7936 (p) cc_final: 0.7506 (m) REVERT: A 163 MET cc_start: 0.6584 (tpp) cc_final: 0.6325 (tpp) REVERT: A 293 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6611 (ptp-170) REVERT: A 324 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 327 SER cc_start: 0.8254 (p) cc_final: 0.8019 (t) REVERT: A 353 PHE cc_start: 0.8189 (p90) cc_final: 0.7622 (p90) REVERT: A 357 ASP cc_start: 0.7846 (t0) cc_final: 0.7387 (t0) REVERT: C 43 GLN cc_start: 0.7430 (mp10) cc_final: 0.6645 (mp10) REVERT: C 48 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6554 (mtp) REVERT: C 98 ARG cc_start: 0.7467 (ttp-170) cc_final: 0.7148 (ttp-170) REVERT: E 83 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7982 (mtmt) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.3922 time to fit residues: 46.2814 Evaluate side-chains 115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 19 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 26 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.158757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144989 restraints weight = 9245.910| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.52 r_work: 0.3830 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6498 Z= 0.168 Angle : 0.604 7.078 8839 Z= 0.305 Chirality : 0.045 0.157 953 Planarity : 0.005 0.048 1130 Dihedral : 4.585 17.090 931 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.58 % Favored : 91.93 % Rotamer: Outliers : 3.77 % Allowed : 15.24 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.62 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 1.05 (0.29), residues: 329 loop : -1.59 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.021 0.002 TYR C 114 PHE 0.013 0.001 PHE F 98 TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 6484) covalent geometry : angle 0.59948 ( 8809) SS BOND : bond 0.00350 ( 12) SS BOND : angle 1.46936 ( 24) hydrogen bonds : bond 0.03064 ( 201) hydrogen bonds : angle 5.78559 ( 567) link_BETA1-4 : bond 0.00197 ( 1) link_BETA1-4 : angle 0.87356 ( 3) link_NAG-ASN : bond 0.00088 ( 1) link_NAG-ASN : angle 0.46220 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7975 (p) cc_final: 0.7550 (m) REVERT: A 163 MET cc_start: 0.6494 (tpp) cc_final: 0.6281 (tpp) REVERT: A 293 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6602 (ptp-170) REVERT: A 310 MET cc_start: 0.6232 (mmp) cc_final: 0.6018 (mmp) REVERT: A 324 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 327 SER cc_start: 0.8259 (p) cc_final: 0.8016 (t) REVERT: A 353 PHE cc_start: 0.8205 (p90) cc_final: 0.7638 (p90) REVERT: A 357 ASP cc_start: 0.7855 (t0) cc_final: 0.7377 (t0) REVERT: C 43 GLN cc_start: 0.7422 (mp10) cc_final: 0.6635 (mp10) REVERT: C 48 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.6557 (mtp) REVERT: C 98 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7161 (ttp-170) REVERT: E 83 LYS cc_start: 0.8259 (mtmt) cc_final: 0.8004 (mtmt) outliers start: 26 outliers final: 12 residues processed: 112 average time/residue: 0.3721 time to fit residues: 44.3851 Evaluate side-chains 115 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 112 GLN Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.157830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.143902 restraints weight = 9192.171| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.54 r_work: 0.3806 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6498 Z= 0.214 Angle : 0.674 13.650 8839 Z= 0.334 Chirality : 0.049 0.452 953 Planarity : 0.005 0.049 1130 Dihedral : 4.832 19.318 931 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.07 % Favored : 91.43 % Rotamer: Outliers : 2.76 % Allowed : 17.42 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.77 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.95 (0.29), residues: 322 loop : -1.66 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.025 0.002 TYR C 114 PHE 0.018 0.002 PHE F 98 TRP 0.013 0.002 TRP A 207 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 6484) covalent geometry : angle 0.66972 ( 8809) SS BOND : bond 0.00407 ( 12) SS BOND : angle 1.55031 ( 24) hydrogen bonds : bond 0.03383 ( 201) hydrogen bonds : angle 5.88944 ( 567) link_BETA1-4 : bond 0.00202 ( 1) link_BETA1-4 : angle 0.89446 ( 3) link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 0.60767 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8047 (p) cc_final: 0.7627 (m) REVERT: A 131 MET cc_start: 0.6549 (tpt) cc_final: 0.6321 (tpt) REVERT: A 191 MET cc_start: 0.7716 (ttp) cc_final: 0.7074 (ttp) REVERT: A 262 LYS cc_start: 0.6979 (tmtt) cc_final: 0.6744 (tmtt) REVERT: A 293 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.6542 (ptp-170) REVERT: A 324 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7769 (p) REVERT: A 327 SER cc_start: 0.8263 (p) cc_final: 0.8010 (t) REVERT: A 353 PHE cc_start: 0.8259 (p90) cc_final: 0.7710 (p90) REVERT: A 357 ASP cc_start: 0.7853 (t0) cc_final: 0.7383 (t0) REVERT: A 426 VAL cc_start: 0.6738 (t) cc_final: 0.6325 (p) REVERT: C 43 GLN cc_start: 0.7418 (mp10) cc_final: 0.6600 (mp10) REVERT: C 48 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6590 (ttp) REVERT: C 98 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7135 (ttp-170) REVERT: E 83 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7943 (mtmt) outliers start: 19 outliers final: 14 residues processed: 114 average time/residue: 0.3901 time to fit residues: 47.2638 Evaluate side-chains 122 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.158821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.145289 restraints weight = 9139.901| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.50 r_work: 0.3833 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6498 Z= 0.138 Angle : 0.612 12.428 8839 Z= 0.305 Chirality : 0.046 0.318 953 Planarity : 0.005 0.045 1130 Dihedral : 4.574 17.248 931 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.34 % Favored : 93.17 % Rotamer: Outliers : 2.18 % Allowed : 18.00 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.74 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.89 (0.29), residues: 325 loop : -1.59 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.016 0.001 TYR C 114 PHE 0.009 0.001 PHE F 98 TRP 0.010 0.001 TRP C 47 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6484) covalent geometry : angle 0.60955 ( 8809) SS BOND : bond 0.00378 ( 12) SS BOND : angle 1.28508 ( 24) hydrogen bonds : bond 0.03035 ( 201) hydrogen bonds : angle 5.72268 ( 567) link_BETA1-4 : bond 0.00229 ( 1) link_BETA1-4 : angle 0.95170 ( 3) link_NAG-ASN : bond 0.00107 ( 1) link_NAG-ASN : angle 0.42207 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7958 (p) cc_final: 0.7538 (m) REVERT: A 262 LYS cc_start: 0.6933 (tmtt) cc_final: 0.6695 (tmtt) REVERT: A 324 THR cc_start: 0.8026 (p) cc_final: 0.7650 (p) REVERT: A 327 SER cc_start: 0.8235 (p) cc_final: 0.7987 (t) REVERT: A 353 PHE cc_start: 0.8219 (p90) cc_final: 0.7754 (p90) REVERT: C 43 GLN cc_start: 0.7414 (mp10) cc_final: 0.6633 (mp10) REVERT: C 48 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6533 (mtp) REVERT: C 98 ARG cc_start: 0.7448 (ttp-170) cc_final: 0.7119 (ttp-170) REVERT: E 83 LYS cc_start: 0.8143 (mtmt) cc_final: 0.7854 (mtmt) outliers start: 15 outliers final: 13 residues processed: 109 average time/residue: 0.4063 time to fit residues: 47.0520 Evaluate side-chains 116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 6 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.143681 restraints weight = 9276.284| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.60 r_work: 0.3807 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6498 Z= 0.197 Angle : 0.664 11.844 8839 Z= 0.330 Chirality : 0.048 0.322 953 Planarity : 0.005 0.049 1130 Dihedral : 4.770 18.717 931 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.70 % Favored : 90.81 % Rotamer: Outliers : 2.32 % Allowed : 18.72 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.81 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.85 (0.29), residues: 326 loop : -1.65 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.023 0.002 TYR C 114 PHE 0.015 0.002 PHE F 98 TRP 0.012 0.001 TRP A 207 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6484) covalent geometry : angle 0.65786 ( 8809) SS BOND : bond 0.00511 ( 12) SS BOND : angle 1.85344 ( 24) hydrogen bonds : bond 0.03306 ( 201) hydrogen bonds : angle 5.80534 ( 567) link_BETA1-4 : bond 0.00186 ( 1) link_BETA1-4 : angle 0.90547 ( 3) link_NAG-ASN : bond 0.00134 ( 1) link_NAG-ASN : angle 0.59729 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8027 (p) cc_final: 0.7632 (m) REVERT: A 262 LYS cc_start: 0.6992 (tmtt) cc_final: 0.6747 (tmtt) REVERT: A 324 THR cc_start: 0.8123 (p) cc_final: 0.7745 (p) REVERT: A 327 SER cc_start: 0.8255 (p) cc_final: 0.8001 (t) REVERT: A 353 PHE cc_start: 0.8271 (p90) cc_final: 0.7731 (p90) REVERT: A 357 ASP cc_start: 0.7901 (t0) cc_final: 0.7507 (t0) REVERT: C 43 GLN cc_start: 0.7423 (mp10) cc_final: 0.6611 (mp10) REVERT: C 48 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6576 (mtp) REVERT: C 98 ARG cc_start: 0.7485 (ttp-170) cc_final: 0.7112 (ttp-170) REVERT: E 83 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7863 (mtmt) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.3917 time to fit residues: 45.3864 Evaluate side-chains 116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS C 6 GLN F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144232 restraints weight = 9100.306| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.53 r_work: 0.3818 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6498 Z= 0.181 Angle : 0.668 11.454 8839 Z= 0.334 Chirality : 0.048 0.301 953 Planarity : 0.005 0.048 1130 Dihedral : 4.773 18.604 931 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.95 % Favored : 91.55 % Rotamer: Outliers : 2.32 % Allowed : 19.74 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.82 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.84 (0.28), residues: 326 loop : -1.66 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.021 0.002 TYR C 114 PHE 0.013 0.001 PHE F 98 TRP 0.011 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 6484) covalent geometry : angle 0.66193 ( 8809) SS BOND : bond 0.00412 ( 12) SS BOND : angle 1.80496 ( 24) hydrogen bonds : bond 0.03278 ( 201) hydrogen bonds : angle 5.80622 ( 567) link_BETA1-4 : bond 0.00163 ( 1) link_BETA1-4 : angle 0.92977 ( 3) link_NAG-ASN : bond 0.00151 ( 1) link_NAG-ASN : angle 0.55319 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1610 Ramachandran restraints generated. 805 Oldfield, 0 Emsley, 805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8020 (p) cc_final: 0.7621 (m) REVERT: A 262 LYS cc_start: 0.6986 (tmtt) cc_final: 0.6746 (tmtt) REVERT: A 324 THR cc_start: 0.8114 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 327 SER cc_start: 0.8241 (p) cc_final: 0.7990 (t) REVERT: C 43 GLN cc_start: 0.7413 (mp10) cc_final: 0.6592 (mp10) REVERT: C 48 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6526 (mtp) REVERT: C 98 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7108 (ttp-170) REVERT: E 83 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7846 (mtmt) outliers start: 16 outliers final: 13 residues processed: 108 average time/residue: 0.3641 time to fit residues: 41.9379 Evaluate side-chains 116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 231 CYS Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.158264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144267 restraints weight = 9204.527| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.57 r_work: 0.3826 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6498 Z= 0.169 Angle : 0.650 11.373 8839 Z= 0.325 Chirality : 0.047 0.275 953 Planarity : 0.005 0.045 1130 Dihedral : 4.723 18.040 931 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.83 % Favored : 91.68 % Rotamer: Outliers : 2.61 % Allowed : 19.16 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.83 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.89 (0.29), residues: 323 loop : -1.69 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 18 TYR 0.021 0.002 TYR C 103 PHE 0.013 0.001 PHE F 98 TRP 0.011 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6484) covalent geometry : angle 0.64522 ( 8809) SS BOND : bond 0.00388 ( 12) SS BOND : angle 1.69384 ( 24) hydrogen bonds : bond 0.03153 ( 201) hydrogen bonds : angle 5.73638 ( 567) link_BETA1-4 : bond 0.00166 ( 1) link_BETA1-4 : angle 0.95471 ( 3) link_NAG-ASN : bond 0.00130 ( 1) link_NAG-ASN : angle 0.54003 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.36 seconds wall clock time: 30 minutes 26.84 seconds (1826.84 seconds total)