Starting phenix.real_space_refine on Sun Apr 27 17:20:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z4e_39762/04_2025/8z4e_39762.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z4e_39762/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z4e_39762/04_2025/8z4e_39762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z4e_39762/04_2025/8z4e_39762.map" model { file = "/net/cci-nas-00/data/ceres_data/8z4e_39762/04_2025/8z4e_39762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z4e_39762/04_2025/8z4e_39762.cif" } resolution = 3.0 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= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.40, per 1000 atoms: 0.70 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: 1.57 Conformation dependent library (CDL) restraints added in 939.1 milliseconds 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: 0.82 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: 2.48 Time building geometry restraints manager: 1.83 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: 2.210 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.120 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- 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 (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: -0.63 (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 TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS A 98 PHE 0.008 0.001 PHE A 132 TYR 0.008 0.001 TYR F 86 ARG 0.004 0.000 ARG A 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 1) link_NAG-ASN : angle 0.42911 ( 3) link_BETA1-4 : bond 0.00218 ( 1) link_BETA1-4 : angle 1.34418 ( 3) hydrogen bonds : bond 0.09536 ( 201) hydrogen bonds : angle 6.94040 ( 567) SS BOND : bond 0.00459 ( 12) SS BOND : angle 1.62686 ( 24) covalent geometry : bond 0.00283 ( 6484) covalent geometry : angle 0.61108 ( 8809) *********************** 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 : 0.606 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: 0.9922 time to fit residues: 108.4619 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 : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.161409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.147984 restraints weight = 9121.091| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.50 r_work: 0.3880 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6498 Z= 0.195 Angle : 0.626 7.155 8839 Z= 0.323 Chirality : 0.046 0.166 953 Planarity : 0.006 0.052 1130 Dihedral : 4.626 30.271 931 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.20 % Favored : 92.30 % Rotamer: Outliers : 1.89 % Allowed : 9.29 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.66 (0.30), residues: 805 helix: -1.95 (1.98), residues: 6 sheet: 1.07 (0.30), residues: 324 loop : -1.63 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 37 HIS 0.006 0.002 HIS A 185 PHE 0.014 0.002 PHE F 98 TYR 0.018 0.002 TYR C 114 ARG 0.004 0.001 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 0.33001 ( 3) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 0.78571 ( 3) hydrogen bonds : bond 0.03261 ( 201) hydrogen bonds : angle 6.05043 ( 567) SS BOND : bond 0.00516 ( 12) SS BOND : angle 1.35899 ( 24) covalent geometry : bond 0.00454 ( 6484) covalent geometry : angle 0.62327 ( 8809) *********************** 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 118 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7819 (p) cc_final: 0.7376 (m) REVERT: A 211 ARG cc_start: 0.7233 (ptt-90) cc_final: 0.6926 (ptt-90) REVERT: A 327 SER cc_start: 0.8260 (p) cc_final: 0.8015 (t) REVERT: B 112 GLN cc_start: 0.6944 (pp30) cc_final: 0.6615 (pp30) REVERT: C 6 GLN cc_start: 0.8188 (mt0) cc_final: 0.7921 (mt0) REVERT: C 98 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7175 (ttp-170) REVERT: E 83 LYS cc_start: 0.8273 (mtmt) cc_final: 0.8021 (mtmt) outliers start: 13 outliers final: 6 residues processed: 106 average time/residue: 0.8860 time to fit residues: 100.3288 Evaluate side-chains 107 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 101 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 4 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.158993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.145018 restraints weight = 9339.483| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.58 r_work: 0.3847 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6498 Z= 0.206 Angle : 0.626 6.842 8839 Z= 0.320 Chirality : 0.046 0.157 953 Planarity : 0.006 0.057 1130 Dihedral : 4.732 17.340 931 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.71 % Favored : 92.80 % Rotamer: Outliers : 2.90 % Allowed : 13.50 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.69 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 1.15 (0.30), residues: 310 loop : -1.65 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 207 HIS 0.006 0.001 HIS A 185 PHE 0.019 0.002 PHE A 353 TYR 0.027 0.002 TYR A 375 ARG 0.006 0.001 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 1) link_NAG-ASN : angle 0.48229 ( 3) link_BETA1-4 : bond 0.00227 ( 1) link_BETA1-4 : angle 0.82415 ( 3) hydrogen bonds : bond 0.03337 ( 201) hydrogen bonds : angle 5.94799 ( 567) SS BOND : bond 0.00376 ( 12) SS BOND : angle 1.40039 ( 24) covalent geometry : bond 0.00485 ( 6484) covalent geometry : angle 0.62274 ( 8809) *********************** 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 119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7966 (p) cc_final: 0.7520 (m) REVERT: A 262 LYS cc_start: 0.6955 (tmtt) cc_final: 0.6710 (tmtt) REVERT: A 293 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6629 (ptp-170) REVERT: A 310 MET cc_start: 0.6331 (mmp) cc_final: 0.6123 (mmp) REVERT: A 327 SER cc_start: 0.8223 (p) cc_final: 0.7990 (t) REVERT: A 353 PHE cc_start: 0.8141 (p90) cc_final: 0.7747 (p90) REVERT: A 357 ASP cc_start: 0.7902 (t0) cc_final: 0.7466 (t0) REVERT: B 112 GLN cc_start: 0.7352 (pp30) cc_final: 0.7121 (pp30) REVERT: C 6 GLN cc_start: 0.8232 (mt0) cc_final: 0.8008 (mt0) REVERT: C 43 GLN cc_start: 0.7341 (mp10) cc_final: 0.6570 (mp10) REVERT: C 48 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6575 (ttp) REVERT: C 98 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7166 (ttp-170) REVERT: E 83 LYS cc_start: 0.8261 (mtmt) cc_final: 0.8028 (mtmt) REVERT: E 86 ASP cc_start: 0.6906 (t0) cc_final: 0.6630 (t0) outliers start: 20 outliers final: 12 residues processed: 105 average time/residue: 1.1773 time to fit residues: 131.6543 Evaluate side-chains 111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 228 GLU 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 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 21 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 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 57 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4125 r_free = 0.4125 target = 0.159306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.145203 restraints weight = 9297.593| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.62 r_work: 0.3847 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6498 Z= 0.158 Angle : 0.588 6.458 8839 Z= 0.302 Chirality : 0.044 0.155 953 Planarity : 0.005 0.052 1130 Dihedral : 4.594 18.990 931 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.21 % Favored : 93.29 % Rotamer: Outliers : 2.90 % Allowed : 14.51 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.62 (0.30), residues: 805 helix: None (None), residues: 0 sheet: 1.08 (0.29), residues: 323 loop : -1.59 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 PHE 0.011 0.001 PHE F 98 TYR 0.020 0.002 TYR C 114 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 0.43385 ( 3) link_BETA1-4 : bond 0.00051 ( 1) link_BETA1-4 : angle 0.78585 ( 3) hydrogen bonds : bond 0.03025 ( 201) hydrogen bonds : angle 5.84375 ( 567) SS BOND : bond 0.00358 ( 12) SS BOND : angle 1.23222 ( 24) covalent geometry : bond 0.00373 ( 6484) covalent geometry : angle 0.58567 ( 8809) *********************** 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 119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7926 (p) cc_final: 0.7483 (m) REVERT: A 262 LYS cc_start: 0.6938 (tmtt) cc_final: 0.6681 (tmtt) REVERT: A 310 MET cc_start: 0.6382 (mmp) cc_final: 0.6153 (mmp) REVERT: A 324 THR cc_start: 0.8153 (p) cc_final: 0.7766 (p) REVERT: A 327 SER cc_start: 0.8266 (p) cc_final: 0.8020 (t) REVERT: A 353 PHE cc_start: 0.8244 (p90) cc_final: 0.7672 (p90) REVERT: B 112 GLN cc_start: 0.7206 (pp30) cc_final: 0.6900 (pp30) REVERT: C 43 GLN cc_start: 0.7346 (mp10) cc_final: 0.6537 (mp10) REVERT: C 48 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6639 (mtp) REVERT: C 98 ARG cc_start: 0.7484 (ttp-170) cc_final: 0.7135 (ttp-170) REVERT: E 83 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7980 (mtmt) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 1.1323 time to fit residues: 128.2111 Evaluate side-chains 111 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 377 MET 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 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 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 40 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 0.0070 chunk 77 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 136 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.159061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144852 restraints weight = 9166.143| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.60 r_work: 0.3819 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6498 Z= 0.188 Angle : 0.609 6.645 8839 Z= 0.311 Chirality : 0.045 0.160 953 Planarity : 0.005 0.049 1130 Dihedral : 4.715 18.112 931 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.33 % Favored : 92.17 % Rotamer: Outliers : 3.19 % Allowed : 15.09 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.67 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.95 (0.29), residues: 334 loop : -1.61 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.005 0.001 HIS A 185 PHE 0.014 0.001 PHE F 98 TYR 0.022 0.002 TYR C 114 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 1) link_NAG-ASN : angle 0.52399 ( 3) link_BETA1-4 : bond 0.00244 ( 1) link_BETA1-4 : angle 0.86117 ( 3) hydrogen bonds : bond 0.03162 ( 201) hydrogen bonds : angle 5.85391 ( 567) SS BOND : bond 0.00449 ( 12) SS BOND : angle 1.64889 ( 24) covalent geometry : bond 0.00440 ( 6484) covalent geometry : angle 0.60354 ( 8809) *********************** 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 130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7996 (p) cc_final: 0.7571 (m) REVERT: A 262 LYS cc_start: 0.6958 (tmtt) cc_final: 0.6706 (tmtt) REVERT: A 293 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6558 (ptp-170) REVERT: A 310 MET cc_start: 0.6322 (mmp) cc_final: 0.6078 (mmp) REVERT: A 324 THR cc_start: 0.8144 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 327 SER cc_start: 0.8267 (p) cc_final: 0.8030 (t) REVERT: A 353 PHE cc_start: 0.8191 (p90) cc_final: 0.7609 (p90) REVERT: C 43 GLN cc_start: 0.7436 (mp10) cc_final: 0.6605 (mp10) REVERT: C 48 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6587 (ttp) REVERT: C 98 ARG cc_start: 0.7492 (ttp-170) cc_final: 0.7153 (ttp-170) REVERT: E 66 ARG cc_start: 0.6711 (ptt90) cc_final: 0.6414 (ptt90) REVERT: E 83 LYS cc_start: 0.8244 (mtmt) cc_final: 0.8000 (mtmt) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 1.0581 time to fit residues: 129.2523 Evaluate side-chains 120 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.699 ------------------------------------------------------------------------------- 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 377 MET Chi-restraints excluded: chain A residue 385 THR 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 Chi-restraints excluded: chain F residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.157956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.144073 restraints weight = 9085.123| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.51 r_work: 0.3815 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6498 Z= 0.205 Angle : 0.640 7.619 8839 Z= 0.323 Chirality : 0.046 0.164 953 Planarity : 0.005 0.050 1130 Dihedral : 4.821 19.257 931 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.70 % Favored : 91.80 % Rotamer: Outliers : 3.63 % Allowed : 16.84 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.75 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.92 (0.29), residues: 326 loop : -1.64 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 207 HIS 0.006 0.001 HIS A 185 PHE 0.016 0.002 PHE F 98 TYR 0.025 0.002 TYR C 114 ARG 0.007 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 1) link_NAG-ASN : angle 0.54698 ( 3) link_BETA1-4 : bond 0.00189 ( 1) link_BETA1-4 : angle 0.85179 ( 3) hydrogen bonds : bond 0.03274 ( 201) hydrogen bonds : angle 5.92127 ( 567) SS BOND : bond 0.00409 ( 12) SS BOND : angle 1.58118 ( 24) covalent geometry : bond 0.00482 ( 6484) covalent geometry : angle 0.63589 ( 8809) *********************** 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 130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8058 (p) cc_final: 0.7655 (m) REVERT: A 262 LYS cc_start: 0.6978 (tmtt) cc_final: 0.6728 (tmtt) REVERT: A 293 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.6547 (ptp-170) REVERT: A 310 MET cc_start: 0.6320 (mmp) cc_final: 0.6096 (mmp) REVERT: A 324 THR cc_start: 0.8136 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 327 SER cc_start: 0.8259 (p) cc_final: 0.8014 (t) REVERT: A 353 PHE cc_start: 0.8202 (p90) cc_final: 0.7674 (p90) REVERT: C 43 GLN cc_start: 0.7333 (mp10) cc_final: 0.6564 (mp10) REVERT: C 48 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.6565 (ttp) REVERT: C 98 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7091 (ttp-170) REVERT: E 83 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7967 (mtmt) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.9789 time to fit residues: 117.8038 Evaluate side-chains 121 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 377 MET Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 448 LEU 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 C residue 91 THR 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 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 63 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.159161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145291 restraints weight = 9126.902| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.53 r_work: 0.3823 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6498 Z= 0.151 Angle : 0.632 13.364 8839 Z= 0.313 Chirality : 0.047 0.412 953 Planarity : 0.005 0.047 1130 Dihedral : 4.647 17.925 931 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.50 % Allowed : 6.58 % Favored : 92.92 % Rotamer: Outliers : 2.76 % Allowed : 16.98 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.73 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.93 (0.29), residues: 326 loop : -1.61 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 37 HIS 0.004 0.001 HIS A 185 PHE 0.010 0.001 PHE F 98 TYR 0.018 0.002 TYR A 375 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 1) link_NAG-ASN : angle 0.44918 ( 3) link_BETA1-4 : bond 0.00219 ( 1) link_BETA1-4 : angle 0.93005 ( 3) hydrogen bonds : bond 0.03077 ( 201) hydrogen bonds : angle 5.79515 ( 567) SS BOND : bond 0.00328 ( 12) SS BOND : angle 1.33745 ( 24) covalent geometry : bond 0.00354 ( 6484) covalent geometry : angle 0.62885 ( 8809) *********************** 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 119 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8004 (p) cc_final: 0.7589 (m) REVERT: A 262 LYS cc_start: 0.6963 (tmtt) cc_final: 0.6723 (tmtt) REVERT: A 310 MET cc_start: 0.6319 (mmp) cc_final: 0.6116 (mmp) REVERT: A 324 THR cc_start: 0.8099 (OUTLIER) cc_final: 0.7716 (p) REVERT: A 327 SER cc_start: 0.8251 (p) cc_final: 0.8002 (t) REVERT: A 353 PHE cc_start: 0.8193 (p90) cc_final: 0.7665 (p90) REVERT: A 357 ASP cc_start: 0.7841 (t0) cc_final: 0.7425 (t0) REVERT: C 43 GLN cc_start: 0.7387 (mp10) cc_final: 0.6618 (mp10) REVERT: C 48 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6541 (mtp) REVERT: C 98 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.7110 (ttp-170) REVERT: E 66 ARG cc_start: 0.6698 (ptt90) cc_final: 0.6426 (ptt90) REVERT: E 83 LYS cc_start: 0.8196 (mtmt) cc_final: 0.7902 (mtmt) REVERT: F 17 ASP cc_start: 0.6993 (m-30) cc_final: 0.6780 (m-30) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 1.0165 time to fit residues: 116.1006 Evaluate side-chains 116 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 377 MET 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 112 GLN 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 23 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.144426 restraints weight = 9136.372| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.54 r_work: 0.3814 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6498 Z= 0.181 Angle : 0.643 12.234 8839 Z= 0.320 Chirality : 0.047 0.361 953 Planarity : 0.005 0.048 1130 Dihedral : 4.715 18.487 931 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.20 % Favored : 91.30 % Rotamer: Outliers : 3.19 % Allowed : 17.56 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.80 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.85 (0.29), residues: 326 loop : -1.64 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 207 HIS 0.005 0.001 HIS A 185 PHE 0.014 0.002 PHE F 98 TYR 0.021 0.002 TYR C 114 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 0.52535 ( 3) link_BETA1-4 : bond 0.00231 ( 1) link_BETA1-4 : angle 0.91681 ( 3) hydrogen bonds : bond 0.03206 ( 201) hydrogen bonds : angle 5.78100 ( 567) SS BOND : bond 0.00359 ( 12) SS BOND : angle 1.43279 ( 24) covalent geometry : bond 0.00427 ( 6484) covalent geometry : angle 0.63992 ( 8809) *********************** 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 128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.8052 (p) cc_final: 0.7638 (m) REVERT: A 262 LYS cc_start: 0.6988 (tmtt) cc_final: 0.6750 (tmtt) REVERT: A 293 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6368 (ptp-170) REVERT: A 324 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7728 (p) REVERT: A 327 SER cc_start: 0.8256 (p) cc_final: 0.8014 (t) REVERT: A 353 PHE cc_start: 0.8222 (p90) cc_final: 0.7683 (p90) REVERT: A 357 ASP cc_start: 0.7848 (t0) cc_final: 0.7420 (t0) REVERT: C 43 GLN cc_start: 0.7392 (mp10) cc_final: 0.6600 (mp10) REVERT: C 48 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6559 (ttp) REVERT: C 98 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7106 (ttp-170) REVERT: C 116 MET cc_start: 0.6212 (OUTLIER) cc_final: 0.4272 (mmt) REVERT: E 66 ARG cc_start: 0.6731 (ptt90) cc_final: 0.6476 (ptt90) REVERT: E 83 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7931 (mtmt) REVERT: F 6 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.5969 (pt0) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 1.1972 time to fit residues: 144.7099 Evaluate side-chains 125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 377 MET 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 96 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 MET Chi-restraints excluded: chain C residue 124 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.158801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.144526 restraints weight = 9208.380| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.66 r_work: 0.3829 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3213 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= 0.173 Angle : 0.659 11.937 8839 Z= 0.327 Chirality : 0.047 0.312 953 Planarity : 0.005 0.046 1130 Dihedral : 4.719 18.406 931 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.70 % Favored : 91.80 % Rotamer: Outliers : 3.48 % Allowed : 18.29 % 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 (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: -0.81 (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 TRP 0.011 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 PHE 0.013 0.001 PHE F 98 TYR 0.020 0.002 TYR C 114 ARG 0.008 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 1) link_NAG-ASN : angle 0.47983 ( 3) link_BETA1-4 : bond 0.00214 ( 1) link_BETA1-4 : angle 0.94325 ( 3) hydrogen bonds : bond 0.03188 ( 201) hydrogen bonds : angle 5.75426 ( 567) SS BOND : bond 0.00419 ( 12) SS BOND : angle 1.75693 ( 24) covalent geometry : bond 0.00410 ( 6484) covalent geometry : angle 0.65307 ( 8809) *********************** 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 131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.690 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7990 (p) cc_final: 0.7594 (m) REVERT: A 191 MET cc_start: 0.7706 (ttp) cc_final: 0.7211 (ttp) REVERT: A 262 LYS cc_start: 0.6995 (tmtt) cc_final: 0.6754 (tmtt) REVERT: A 293 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6364 (ptp-170) REVERT: A 324 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7700 (p) REVERT: A 327 SER cc_start: 0.8281 (p) cc_final: 0.8033 (t) REVERT: A 353 PHE cc_start: 0.8257 (p90) cc_final: 0.7678 (p90) REVERT: A 357 ASP cc_start: 0.7823 (t0) cc_final: 0.7363 (t0) REVERT: C 43 GLN cc_start: 0.7401 (mp10) cc_final: 0.6567 (mp10) REVERT: C 48 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6591 (ttp) REVERT: C 98 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7097 (ttp-170) REVERT: C 116 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.4229 (mmt) REVERT: E 66 ARG cc_start: 0.6707 (ptt90) cc_final: 0.6480 (ptt90) REVERT: E 83 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7875 (mtmt) REVERT: F 6 GLN cc_start: 0.6325 (OUTLIER) cc_final: 0.5966 (pt0) outliers start: 24 outliers final: 16 residues processed: 117 average time/residue: 0.8838 time to fit residues: 110.3645 Evaluate side-chains 125 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 377 MET 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 96 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 116 MET 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 15 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 3 optimal weight: 0.0050 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.159037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145111 restraints weight = 9300.272| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.63 r_work: 0.3832 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6498 Z= 0.162 Angle : 0.661 11.448 8839 Z= 0.328 Chirality : 0.047 0.285 953 Planarity : 0.005 0.047 1130 Dihedral : 4.670 17.860 931 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.58 % Favored : 91.93 % Rotamer: Outliers : 3.19 % Allowed : 18.58 % 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 (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: -0.79 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.88 (0.29), residues: 325 loop : -1.65 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 37 HIS 0.005 0.001 HIS A 185 PHE 0.012 0.001 PHE F 98 TYR 0.018 0.001 TYR C 114 ARG 0.007 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 1) link_NAG-ASN : angle 0.47368 ( 3) link_BETA1-4 : bond 0.00084 ( 1) link_BETA1-4 : angle 0.92709 ( 3) hydrogen bonds : bond 0.03104 ( 201) hydrogen bonds : angle 5.66468 ( 567) SS BOND : bond 0.00374 ( 12) SS BOND : angle 1.70379 ( 24) covalent geometry : bond 0.00384 ( 6484) covalent geometry : angle 0.65624 ( 8809) ********************** 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 128 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 94 VAL cc_start: 0.7970 (p) cc_final: 0.7578 (m) REVERT: A 131 MET cc_start: 0.6585 (tpt) cc_final: 0.6332 (tpt) REVERT: A 191 MET cc_start: 0.7703 (ttp) cc_final: 0.7179 (ttp) REVERT: A 262 LYS cc_start: 0.6991 (tmtt) cc_final: 0.6750 (tmtt) REVERT: A 293 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6294 (ptp-170) REVERT: A 324 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 327 SER cc_start: 0.8268 (p) cc_final: 0.8022 (t) REVERT: A 353 PHE cc_start: 0.8251 (p90) cc_final: 0.7669 (p90) REVERT: C 43 GLN cc_start: 0.7407 (mp10) cc_final: 0.6595 (mp10) REVERT: C 48 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.6579 (mtp) REVERT: C 98 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7084 (ttp-170) REVERT: C 116 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.4303 (mmt) REVERT: E 66 ARG cc_start: 0.6689 (ptt90) cc_final: 0.6465 (ptt90) REVERT: E 83 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7839 (mtmt) REVERT: F 6 GLN cc_start: 0.6250 (OUTLIER) cc_final: 0.5984 (pt0) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 1.1680 time to fit residues: 144.1734 Evaluate side-chains 126 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU 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 377 MET 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 96 SER Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 116 MET 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 63 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.144998 restraints weight = 9383.607| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.65 r_work: 0.3822 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3329 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= 0.164 Angle : 0.660 11.147 8839 Z= 0.328 Chirality : 0.046 0.266 953 Planarity : 0.005 0.045 1130 Dihedral : 4.682 18.148 931 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.20 % Favored : 92.30 % Rotamer: Outliers : 3.19 % Allowed : 19.16 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.13 % 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: -0.82 (0.29), residues: 805 helix: None (None), residues: 0 sheet: 0.78 (0.28), residues: 338 loop : -1.66 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 37 HIS 0.004 0.001 HIS A 185 PHE 0.012 0.001 PHE F 98 TYR 0.021 0.002 TYR C 103 ARG 0.006 0.000 ARG F 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00111 ( 1) link_NAG-ASN : angle 0.49475 ( 3) link_BETA1-4 : bond 0.00227 ( 1) link_BETA1-4 : angle 0.98499 ( 3) hydrogen bonds : bond 0.03072 ( 201) hydrogen bonds : angle 5.66088 ( 567) SS BOND : bond 0.00380 ( 12) SS BOND : angle 1.64651 ( 24) covalent geometry : bond 0.00389 ( 6484) covalent geometry : angle 0.65526 ( 8809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4549.36 seconds wall clock time: 81 minutes 38.94 seconds (4898.94 seconds total)