Starting phenix.real_space_refine on Sun Apr 27 08:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3z_62799/04_2025/9l3z_62799.cif" } resolution = 3.9 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= 0.004 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3242 2.51 5 N 880 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5147 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1531 Classifications: {'peptide': 203} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1379 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 170} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2213 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'PTRANS': 12, 'TRANS': 335} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 568 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 472 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 14, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 268 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Classifications: {'peptide': 1} Modifications used: {'PEPT-D': 1} Time building chain proxies: 3.85, per 1000 atoms: 0.75 Number of scatterers: 5147 At special positions: 0 Unit cell: (66.402, 87.822, 146.727, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 1006 8.00 N 880 7.00 C 3242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " 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 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTR C 2 " Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 11 sheets defined 37.8% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'H' and resid 107 through 112 removed outlier: 3.824A pdb=" N TRP H 111 " --> pdb=" O GLY H 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 67 removed outlier: 3.586A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 91 removed outlier: 3.897A pdb=" N PHE A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Processing helix chain 'A' and resid 143 through 148 removed outlier: 4.561A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 168 removed outlier: 4.747A pdb=" N TRP A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 221 through 229 Processing helix chain 'A' and resid 229 through 274 removed outlier: 4.143A pdb=" N ASP A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 298 removed outlier: 3.926A pdb=" N ASP A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 336 removed outlier: 3.574A pdb=" N LEU A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 removed outlier: 3.640A pdb=" N GLN A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 375 through 393 removed outlier: 3.682A pdb=" N CYS A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) Proline residue: A 389 - end of helix removed outlier: 3.587A pdb=" N LEU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 4.315A pdb=" N THR A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 8 removed outlier: 3.590A pdb=" N GLN H 6 " --> pdb=" O SER H 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 3.503A pdb=" N THR H 121 " --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR H 97 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.797A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.718A pdb=" N LEU H 138 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 150 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.718A pdb=" N LEU H 138 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY H 153 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 150 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL H 198 " --> pdb=" O ALA H 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 165 through 168 Processing sheet with id=AA7, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.653A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 11 through 12 removed outlier: 6.760A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.527A pdb=" N SER L 116 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 146 through 149 removed outlier: 3.645A pdb=" N LYS L 147 " --> pdb=" O THR L 199 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR L 199 " --> pdb=" O LYS L 147 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 164 through 165 265 hydrogen bonds defined for protein. 747 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: 1.37 Time building geometry restraints manager: 1.51 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: 1688 1.34 - 1.46: 1100 1.46 - 1.58: 2432 1.58 - 1.69: 0 1.69 - 1.81: 25 Bond restraints: 5245 Sorted by residual: bond pdb=" N ARG A 252 " pdb=" CA ARG A 252 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.22e+00 bond pdb=" N ASN A 250 " pdb=" CA ASN A 250 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.99e+00 bond pdb=" N ARG A 253 " pdb=" CA ARG A 253 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.42e-02 4.96e+03 4.35e+00 bond pdb=" C GLU H 162 " pdb=" N PRO H 163 " ideal model delta sigma weight residual 1.332 1.354 -0.022 1.12e-02 7.97e+03 3.79e+00 bond pdb=" N ALA A 251 " pdb=" CA ALA A 251 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.28e+00 ... (remaining 5240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 7051 1.71 - 3.42: 97 3.42 - 5.13: 18 5.13 - 6.84: 5 6.84 - 8.56: 1 Bond angle restraints: 7172 Sorted by residual: angle pdb=" CA PRO A 427 " pdb=" N PRO A 427 " pdb=" CD PRO A 427 " ideal model delta sigma weight residual 112.00 107.71 4.29 1.40e+00 5.10e-01 9.38e+00 angle pdb=" C SER H 217 " pdb=" N ASN H 218 " pdb=" CA ASN H 218 " ideal model delta sigma weight residual 122.46 126.76 -4.30 1.41e+00 5.03e-01 9.30e+00 angle pdb=" C SER L 51 " pdb=" N ALA L 52 " pdb=" CA ALA L 52 " ideal model delta sigma weight residual 121.54 127.24 -5.70 1.91e+00 2.74e-01 8.90e+00 angle pdb=" N ARG A 253 " pdb=" CA ARG A 253 " pdb=" C ARG A 253 " ideal model delta sigma weight residual 113.19 109.68 3.51 1.19e+00 7.06e-01 8.68e+00 angle pdb=" N ASN A 250 " pdb=" CA ASN A 250 " pdb=" C ASN A 250 " ideal model delta sigma weight residual 110.97 107.87 3.10 1.09e+00 8.42e-01 8.11e+00 ... (remaining 7167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 2765 16.84 - 33.67: 254 33.67 - 50.51: 58 50.51 - 67.35: 10 67.35 - 84.18: 4 Dihedral angle restraints: 3091 sinusoidal: 958 harmonic: 2133 Sorted by residual: dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual 93.00 59.72 33.28 1 1.00e+01 1.00e-02 1.57e+01 dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual -86.00 -114.07 28.07 1 1.00e+01 1.00e-02 1.13e+01 dihedral pdb=" CA ASP L 2 " pdb=" CB ASP L 2 " pdb=" CG ASP L 2 " pdb=" OD1 ASP L 2 " ideal model delta sinusoidal sigma weight residual -30.00 -86.97 56.97 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 3088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 571 0.036 - 0.071: 208 0.071 - 0.107: 58 0.107 - 0.143: 14 0.143 - 0.178: 2 Chirality restraints: 853 Sorted by residual: chirality pdb=" CA ASP A 305 " pdb=" N ASP A 305 " pdb=" C ASP A 305 " pdb=" CB ASP A 305 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ASN H 218 " pdb=" N ASN H 218 " pdb=" C ASN H 218 " pdb=" CB ASN H 218 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 850 not shown) Planarity restraints: 923 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 115 " -0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C SER A 115 " 0.037 2.00e-02 2.50e+03 pdb=" O SER A 115 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN A 116 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 310 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 311 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 311 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 311 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO L 60 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.022 5.00e-02 4.00e+02 ... (remaining 920 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 880 2.76 - 3.47: 7185 3.47 - 4.19: 11153 4.19 - 4.90: 19642 Nonbonded interactions: 38861 Sorted by model distance: nonbonded pdb=" C HIS C 1 " pdb=" N DTR C 2 " model vdw 1.337 3.350 nonbonded pdb=" OD1 ASP A 315 " pdb=" OH TYR A 356 " model vdw 2.115 3.040 nonbonded pdb=" OD1 ASP L 83 " pdb=" OH TYR L 87 " model vdw 2.173 3.040 nonbonded pdb=" O GLY H 103 " pdb=" OH TYR L 95 " model vdw 2.233 3.040 nonbonded pdb=" O HIS C 1 " pdb=" N DTR C 2 " model vdw 2.260 3.120 ... (remaining 38856 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.380 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 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 0.065 5249 Z= 0.140 Angle : 0.542 8.556 7180 Z= 0.298 Chirality : 0.041 0.178 853 Planarity : 0.004 0.041 923 Dihedral : 14.170 84.183 1687 Min Nonbonded Distance : 1.337 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.21 % Allowed : 12.90 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.34), residues: 700 helix: 0.83 (0.35), residues: 242 sheet: -0.45 (0.46), residues: 151 loop : -0.89 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 PHE 0.006 0.001 PHE H 35 TYR 0.015 0.001 TYR L 92 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.26532 ( 257) hydrogen bonds : angle 8.54911 ( 747) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.36369 ( 8) covalent geometry : bond 0.00278 ( 5245) covalent geometry : angle 0.54231 ( 7172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: L 50 TYR cc_start: 0.8353 (p90) cc_final: 0.8052 (p90) REVERT: L 137 LEU cc_start: 0.8636 (tp) cc_final: 0.8110 (tp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1541 time to fit residues: 24.5815 Evaluate side-chains 106 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.0020 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 overall best weight: 0.2846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.134854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.124119 restraints weight = 10704.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126287 restraints weight = 6746.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.127759 restraints weight = 4636.697| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5249 Z= 0.133 Angle : 0.577 8.844 7180 Z= 0.300 Chirality : 0.043 0.158 853 Planarity : 0.004 0.042 923 Dihedral : 3.988 35.759 760 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.17 % Allowed : 16.70 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.34), residues: 700 helix: 1.90 (0.34), residues: 247 sheet: -0.19 (0.44), residues: 157 loop : -1.10 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 39 HIS 0.003 0.001 HIS C 1 PHE 0.014 0.001 PHE L 120 TYR 0.026 0.002 TYR L 142 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.05630 ( 257) hydrogen bonds : angle 5.30812 ( 747) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.50381 ( 8) covalent geometry : bond 0.00267 ( 5245) covalent geometry : angle 0.57697 ( 7172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8220 (mp0) cc_final: 0.7933 (mp0) REVERT: L 50 TYR cc_start: 0.8408 (p90) cc_final: 0.7903 (p90) REVERT: L 77 SER cc_start: 0.7964 (p) cc_final: 0.7588 (t) REVERT: L 137 LEU cc_start: 0.8441 (tp) cc_final: 0.8133 (tp) REVERT: L 142 TYR cc_start: 0.6585 (t80) cc_final: 0.5965 (t80) REVERT: A 333 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7952 (tt) outliers start: 15 outliers final: 9 residues processed: 118 average time/residue: 0.2156 time to fit residues: 33.6108 Evaluate side-chains 107 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 HIS A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118059 restraints weight = 10639.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120536 restraints weight = 6455.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122283 restraints weight = 4346.435| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 5249 Z= 0.265 Angle : 0.683 6.840 7180 Z= 0.364 Chirality : 0.046 0.150 853 Planarity : 0.005 0.057 923 Dihedral : 4.806 42.362 760 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.86 % Allowed : 19.24 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.34), residues: 700 helix: 1.26 (0.33), residues: 248 sheet: -0.33 (0.42), residues: 164 loop : -1.03 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 105 HIS 0.005 0.002 HIS A 318 PHE 0.014 0.002 PHE A 316 TYR 0.020 0.003 TYR A 356 ARG 0.003 0.001 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.05271 ( 257) hydrogen bonds : angle 5.27077 ( 747) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.59651 ( 8) covalent geometry : bond 0.00591 ( 5245) covalent geometry : angle 0.68353 ( 7172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7991 (m-80) cc_final: 0.7599 (m-10) REVERT: H 134 SER cc_start: 0.8478 (m) cc_final: 0.7942 (p) REVERT: L 50 TYR cc_start: 0.8328 (p90) cc_final: 0.7931 (p90) REVERT: L 77 SER cc_start: 0.8187 (p) cc_final: 0.7805 (t) REVERT: A 416 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6995 (t) outliers start: 23 outliers final: 17 residues processed: 114 average time/residue: 0.1539 time to fit residues: 23.0887 Evaluate side-chains 112 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 416 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.0470 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122657 restraints weight = 11034.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125124 restraints weight = 6634.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126816 restraints weight = 4431.416| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5249 Z= 0.134 Angle : 0.578 6.885 7180 Z= 0.298 Chirality : 0.043 0.146 853 Planarity : 0.004 0.043 923 Dihedral : 4.361 37.010 760 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.50 % Allowed : 20.30 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.34), residues: 700 helix: 1.89 (0.34), residues: 248 sheet: -0.26 (0.43), residues: 158 loop : -1.03 (0.40), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 PHE 0.013 0.001 PHE L 120 TYR 0.017 0.002 TYR A 356 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04030 ( 257) hydrogen bonds : angle 4.76815 ( 747) SS BOND : bond 0.00201 ( 4) SS BOND : angle 0.46326 ( 8) covalent geometry : bond 0.00290 ( 5245) covalent geometry : angle 0.57806 ( 7172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7888 (m-80) cc_final: 0.7466 (m-10) REVERT: H 116 TYR cc_start: 0.8112 (m-80) cc_final: 0.7710 (m-10) REVERT: H 134 SER cc_start: 0.8371 (m) cc_final: 0.7655 (p) REVERT: L 48 LEU cc_start: 0.9072 (mt) cc_final: 0.8838 (mm) REVERT: L 50 TYR cc_start: 0.8297 (p90) cc_final: 0.7889 (p90) REVERT: L 77 SER cc_start: 0.8086 (p) cc_final: 0.7647 (t) outliers start: 26 outliers final: 18 residues processed: 117 average time/residue: 0.1639 time to fit residues: 25.3399 Evaluate side-chains 113 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 91 PHE Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0020 chunk 62 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124311 restraints weight = 10974.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.126695 restraints weight = 6652.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.128326 restraints weight = 4463.205| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5249 Z= 0.117 Angle : 0.563 6.856 7180 Z= 0.288 Chirality : 0.042 0.156 853 Planarity : 0.004 0.042 923 Dihedral : 4.086 31.942 760 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.50 % Allowed : 21.78 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.34), residues: 700 helix: 2.12 (0.34), residues: 248 sheet: -0.10 (0.43), residues: 156 loop : -1.12 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 PHE 0.021 0.002 PHE L 120 TYR 0.017 0.002 TYR A 356 ARG 0.002 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 257) hydrogen bonds : angle 4.52107 ( 747) SS BOND : bond 0.00184 ( 4) SS BOND : angle 0.33824 ( 8) covalent geometry : bond 0.00249 ( 5245) covalent geometry : angle 0.56274 ( 7172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7855 (m-80) cc_final: 0.7408 (m-10) REVERT: H 116 TYR cc_start: 0.8103 (m-80) cc_final: 0.7872 (m-80) REVERT: H 134 SER cc_start: 0.8400 (m) cc_final: 0.7687 (p) REVERT: H 194 SER cc_start: 0.7979 (t) cc_final: 0.7714 (m) REVERT: L 48 LEU cc_start: 0.9033 (mt) cc_final: 0.8827 (mm) REVERT: L 50 TYR cc_start: 0.8231 (p90) cc_final: 0.7845 (p90) REVERT: L 77 SER cc_start: 0.8119 (p) cc_final: 0.7680 (t) outliers start: 26 outliers final: 20 residues processed: 118 average time/residue: 0.1542 time to fit residues: 24.1573 Evaluate side-chains 126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.0370 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.8238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121552 restraints weight = 10916.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123960 restraints weight = 6597.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125616 restraints weight = 4429.278| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5249 Z= 0.163 Angle : 0.597 7.321 7180 Z= 0.308 Chirality : 0.043 0.157 853 Planarity : 0.004 0.043 923 Dihedral : 4.290 32.221 760 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.92 % Allowed : 21.14 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.34), residues: 700 helix: 1.87 (0.33), residues: 248 sheet: -0.13 (0.42), residues: 158 loop : -1.14 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.005 0.001 HIS C 1 PHE 0.015 0.002 PHE L 120 TYR 0.017 0.002 TYR A 356 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03960 ( 257) hydrogen bonds : angle 4.58354 ( 747) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.43543 ( 8) covalent geometry : bond 0.00362 ( 5245) covalent geometry : angle 0.59689 ( 7172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7875 (m-80) cc_final: 0.7408 (m-10) REVERT: H 116 TYR cc_start: 0.8268 (m-80) cc_final: 0.7951 (m-10) REVERT: H 134 SER cc_start: 0.8346 (m) cc_final: 0.7756 (p) REVERT: L 48 LEU cc_start: 0.9023 (mt) cc_final: 0.8812 (mm) REVERT: L 50 TYR cc_start: 0.8256 (p90) cc_final: 0.7853 (p90) REVERT: L 77 SER cc_start: 0.8168 (p) cc_final: 0.7682 (t) outliers start: 28 outliers final: 20 residues processed: 124 average time/residue: 0.1787 time to fit residues: 30.2876 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 245 CYS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 22 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.121728 restraints weight = 10758.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.124094 restraints weight = 6509.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125739 restraints weight = 4372.102| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5249 Z= 0.156 Angle : 0.599 7.060 7180 Z= 0.307 Chirality : 0.043 0.151 853 Planarity : 0.005 0.053 923 Dihedral : 4.236 28.727 760 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.50 % Allowed : 22.41 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 700 helix: 2.05 (0.33), residues: 247 sheet: -0.06 (0.43), residues: 156 loop : -1.22 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.003 0.001 HIS C 1 PHE 0.012 0.002 PHE A 88 TYR 0.023 0.002 TYR L 94 ARG 0.002 0.000 ARG A 137 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 257) hydrogen bonds : angle 4.54649 ( 747) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.49449 ( 8) covalent geometry : bond 0.00347 ( 5245) covalent geometry : angle 0.59868 ( 7172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7846 (m-80) cc_final: 0.7377 (m-10) REVERT: H 116 TYR cc_start: 0.8293 (m-80) cc_final: 0.7998 (m-10) REVERT: L 48 LEU cc_start: 0.9045 (mt) cc_final: 0.8824 (mm) REVERT: L 50 TYR cc_start: 0.8277 (p90) cc_final: 0.7848 (p90) REVERT: L 77 SER cc_start: 0.8103 (p) cc_final: 0.7633 (t) REVERT: L 80 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7659 (mm110) REVERT: L 203 LEU cc_start: 0.7598 (mp) cc_final: 0.7362 (mt) outliers start: 26 outliers final: 22 residues processed: 120 average time/residue: 0.2511 time to fit residues: 40.6343 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.0070 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121311 restraints weight = 10818.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123937 restraints weight = 6345.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125723 restraints weight = 4166.250| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5249 Z= 0.147 Angle : 0.602 7.361 7180 Z= 0.305 Chirality : 0.043 0.193 853 Planarity : 0.006 0.128 923 Dihedral : 4.254 28.934 760 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.29 % Allowed : 22.83 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.34), residues: 700 helix: 2.14 (0.34), residues: 247 sheet: -0.07 (0.43), residues: 156 loop : -1.21 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 164 HIS 0.003 0.001 HIS C 1 PHE 0.011 0.001 PHE L 120 TYR 0.019 0.002 TYR A 356 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 257) hydrogen bonds : angle 4.49238 ( 747) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.35892 ( 8) covalent geometry : bond 0.00327 ( 5245) covalent geometry : angle 0.60204 ( 7172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7883 (m-80) cc_final: 0.7439 (m-10) REVERT: H 116 TYR cc_start: 0.8360 (m-80) cc_final: 0.8018 (m-10) REVERT: L 48 LEU cc_start: 0.9012 (mt) cc_final: 0.8784 (mm) REVERT: L 50 TYR cc_start: 0.8268 (p90) cc_final: 0.7805 (p90) REVERT: L 77 SER cc_start: 0.8174 (p) cc_final: 0.7754 (t) REVERT: L 203 LEU cc_start: 0.7649 (mp) cc_final: 0.7408 (mt) REVERT: A 353 ARG cc_start: 0.6617 (ptm-80) cc_final: 0.6003 (ptm160) outliers start: 25 outliers final: 22 residues processed: 121 average time/residue: 0.2017 time to fit residues: 32.8818 Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 36 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 16 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 168 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.123971 restraints weight = 10873.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126420 restraints weight = 6557.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.128078 restraints weight = 4353.578| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5249 Z= 0.118 Angle : 0.593 8.886 7180 Z= 0.296 Chirality : 0.042 0.184 853 Planarity : 0.005 0.089 923 Dihedral : 4.086 24.879 760 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.50 % Allowed : 23.68 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.34), residues: 700 helix: 2.30 (0.34), residues: 247 sheet: 0.09 (0.43), residues: 156 loop : -1.22 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 PHE 0.010 0.001 PHE A 88 TYR 0.017 0.001 TYR A 356 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 257) hydrogen bonds : angle 4.29749 ( 747) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.37840 ( 8) covalent geometry : bond 0.00256 ( 5245) covalent geometry : angle 0.59307 ( 7172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7814 (m-80) cc_final: 0.7375 (m-10) REVERT: H 116 TYR cc_start: 0.8224 (m-80) cc_final: 0.8001 (m-80) REVERT: H 194 SER cc_start: 0.8048 (t) cc_final: 0.7782 (m) REVERT: L 48 LEU cc_start: 0.9039 (mt) cc_final: 0.8831 (mm) REVERT: L 50 TYR cc_start: 0.8227 (p90) cc_final: 0.7805 (p90) REVERT: L 77 SER cc_start: 0.8081 (p) cc_final: 0.7615 (t) REVERT: A 348 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6411 (pp30) outliers start: 26 outliers final: 21 residues processed: 125 average time/residue: 0.2094 time to fit residues: 33.9889 Evaluate side-chains 131 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122443 restraints weight = 10931.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124850 restraints weight = 6582.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126481 restraints weight = 4387.904| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5249 Z= 0.150 Angle : 0.621 8.757 7180 Z= 0.312 Chirality : 0.043 0.199 853 Planarity : 0.005 0.092 923 Dihedral : 4.180 25.186 760 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 5.07 % Allowed : 23.47 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.34), residues: 700 helix: 2.22 (0.34), residues: 247 sheet: 0.12 (0.43), residues: 156 loop : -1.26 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 262 HIS 0.003 0.001 HIS C 1 PHE 0.011 0.001 PHE A 88 TYR 0.018 0.002 TYR A 356 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 257) hydrogen bonds : angle 4.34966 ( 747) SS BOND : bond 0.00531 ( 4) SS BOND : angle 0.37309 ( 8) covalent geometry : bond 0.00335 ( 5245) covalent geometry : angle 0.62090 ( 7172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7833 (m-80) cc_final: 0.7389 (m-10) REVERT: H 86 MET cc_start: 0.8164 (tpp) cc_final: 0.7879 (mmm) REVERT: L 48 LEU cc_start: 0.9042 (mt) cc_final: 0.8831 (mm) REVERT: L 50 TYR cc_start: 0.8225 (p90) cc_final: 0.7274 (p90) REVERT: L 54 SER cc_start: 0.9315 (m) cc_final: 0.9100 (p) REVERT: L 77 SER cc_start: 0.8121 (p) cc_final: 0.7671 (t) REVERT: A 348 GLN cc_start: 0.6886 (OUTLIER) cc_final: 0.6443 (pp30) outliers start: 24 outliers final: 23 residues processed: 120 average time/residue: 0.2181 time to fit residues: 34.5988 Evaluate side-chains 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 130 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 387 TRP Chi-restraints excluded: chain A residue 394 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 70 optimal weight: 0.0000 chunk 41 optimal weight: 0.7980 chunk 68 optimal weight: 0.0870 chunk 54 optimal weight: 0.7980 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125182 restraints weight = 10984.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127607 restraints weight = 6557.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.129292 restraints weight = 4354.534| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5249 Z= 0.115 Angle : 0.595 8.920 7180 Z= 0.295 Chirality : 0.042 0.181 853 Planarity : 0.005 0.072 923 Dihedral : 3.959 22.178 760 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.65 % Allowed : 23.89 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.34), residues: 700 helix: 2.41 (0.34), residues: 247 sheet: 0.28 (0.44), residues: 156 loop : -1.26 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 PHE 0.011 0.001 PHE A 88 TYR 0.016 0.001 TYR A 356 ARG 0.003 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03247 ( 257) hydrogen bonds : angle 4.17861 ( 747) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.30619 ( 8) covalent geometry : bond 0.00252 ( 5245) covalent geometry : angle 0.59533 ( 7172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2314.14 seconds wall clock time: 42 minutes 58.45 seconds (2578.45 seconds total)