Starting phenix.real_space_refine on Sat May 10 04:57:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3z_62799/05_2025/9l3z_62799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3z_62799/05_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_62799/05_2025/9l3z_62799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3z_62799/05_2025/9l3z_62799.map" model { file = "/net/cci-nas-00/data/ceres_data/9l3z_62799/05_2025/9l3z_62799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3z_62799/05_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 4.29, per 1000 atoms: 0.83 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: 1.30 Conformation dependent library (CDL) restraints added in 702.2 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: 0.52 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: 1.40 Time building geometry restraints manager: 1.53 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: 1.270 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.350 Find NCS groups from input model: 0.070 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:3.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.680 ------------------------------------------------------------------------------- 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 : 0.516 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: 0.1480 time to fit residues: 23.4191 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 : 0.503 ------------------------------------------------------------------------------- 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: 0.6980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 overall best weight: 0.3146 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.135269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.124581 restraints weight = 10684.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.126733 restraints weight = 6732.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128212 restraints weight = 4633.870| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5249 Z= 0.131 Angle : 0.581 8.862 7180 Z= 0.302 Chirality : 0.043 0.161 853 Planarity : 0.005 0.042 923 Dihedral : 4.018 33.858 760 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.96 % Allowed : 16.70 % Favored : 80.34 % 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: 1.91 (0.33), residues: 248 sheet: -0.21 (0.44), residues: 157 loop : -1.10 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 39 HIS 0.001 0.001 HIS H 38 PHE 0.015 0.001 PHE L 120 TYR 0.028 0.002 TYR L 142 ARG 0.003 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 257) hydrogen bonds : angle 5.18952 ( 747) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.56974 ( 8) covalent geometry : bond 0.00271 ( 5245) covalent geometry : angle 0.58100 ( 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 127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: H 9 GLU cc_start: 0.8200 (mp0) cc_final: 0.7878 (mp0) REVERT: L 50 TYR cc_start: 0.8399 (p90) cc_final: 0.7863 (p90) REVERT: L 77 SER cc_start: 0.8025 (p) cc_final: 0.7663 (t) REVERT: L 137 LEU cc_start: 0.8409 (tp) cc_final: 0.8119 (tp) REVERT: L 142 TYR cc_start: 0.6631 (t80) cc_final: 0.6026 (t80) REVERT: A 333 LEU cc_start: 0.8243 (tp) cc_final: 0.7982 (tt) outliers start: 14 outliers final: 9 residues processed: 121 average time/residue: 0.1619 time to fit residues: 25.3021 Evaluate side-chains 108 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 24 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.0060 chunk 37 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.137236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125437 restraints weight = 10757.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127884 restraints weight = 6485.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129533 restraints weight = 4333.915| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5249 Z= 0.144 Angle : 0.566 6.286 7180 Z= 0.296 Chirality : 0.043 0.144 853 Planarity : 0.004 0.042 923 Dihedral : 4.035 33.975 760 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.65 % Allowed : 18.39 % Favored : 76.96 % 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: 0.45 (0.34), residues: 700 helix: 1.99 (0.34), residues: 248 sheet: -0.00 (0.45), residues: 156 loop : -1.00 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 168 HIS 0.003 0.001 HIS L 200 PHE 0.013 0.001 PHE A 88 TYR 0.022 0.002 TYR L 94 ARG 0.002 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 257) hydrogen bonds : angle 4.76581 ( 747) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.46259 ( 8) covalent geometry : bond 0.00318 ( 5245) covalent geometry : angle 0.56609 ( 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 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7952 (m-80) cc_final: 0.7563 (m-10) REVERT: L 50 TYR cc_start: 0.8292 (p90) cc_final: 0.7875 (p90) REVERT: L 77 SER cc_start: 0.8122 (p) cc_final: 0.7735 (t) REVERT: L 142 TYR cc_start: 0.6783 (t80) cc_final: 0.6249 (t80) outliers start: 22 outliers final: 15 residues processed: 112 average time/residue: 0.1606 time to fit residues: 23.4259 Evaluate side-chains 115 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 TYR Chi-restraints excluded: chain H residue 94 THR 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 165 VAL Chi-restraints excluded: chain L residue 198 VAL 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 394 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 67 optimal weight: 0.0980 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.133775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122505 restraints weight = 10959.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124868 restraints weight = 6574.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126490 restraints weight = 4387.146| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5249 Z= 0.183 Angle : 0.611 8.610 7180 Z= 0.314 Chirality : 0.043 0.152 853 Planarity : 0.004 0.043 923 Dihedral : 4.290 37.381 760 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.44 % Allowed : 20.51 % Favored : 75.05 % 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: 1.93 (0.33), residues: 248 sheet: -0.10 (0.44), residues: 158 loop : -1.10 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 164 HIS 0.004 0.001 HIS C 1 PHE 0.013 0.001 PHE A 88 TYR 0.018 0.002 TYR A 356 ARG 0.001 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.04234 ( 257) hydrogen bonds : angle 4.75741 ( 747) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.53179 ( 8) covalent geometry : bond 0.00407 ( 5245) covalent geometry : angle 0.61151 ( 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 124 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7914 (m-80) cc_final: 0.7501 (m-10) REVERT: H 116 TYR cc_start: 0.8125 (m-80) cc_final: 0.7834 (m-80) REVERT: H 134 SER cc_start: 0.8457 (m) cc_final: 0.7896 (p) REVERT: L 48 LEU cc_start: 0.9064 (mt) cc_final: 0.8823 (mm) REVERT: L 50 TYR cc_start: 0.8294 (p90) cc_final: 0.7938 (p90) REVERT: L 77 SER cc_start: 0.8109 (p) cc_final: 0.7718 (t) REVERT: L 80 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7803 (mm110) outliers start: 21 outliers final: 17 residues processed: 116 average time/residue: 0.1532 time to fit residues: 23.2456 Evaluate side-chains 117 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 112 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- 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 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119469 restraints weight = 10809.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.122035 restraints weight = 6388.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123734 restraints weight = 4221.005| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5249 Z= 0.210 Angle : 0.625 7.162 7180 Z= 0.325 Chirality : 0.044 0.162 853 Planarity : 0.005 0.045 923 Dihedral : 4.523 37.374 760 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.71 % Allowed : 22.20 % 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: 0.10 (0.34), residues: 700 helix: 1.72 (0.33), residues: 248 sheet: -0.24 (0.43), residues: 158 loop : -1.20 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 164 HIS 0.005 0.002 HIS C 1 PHE 0.015 0.002 PHE H 71 TYR 0.020 0.002 TYR A 356 ARG 0.003 0.000 ARG H 70 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 257) hydrogen bonds : angle 4.82640 ( 747) SS BOND : bond 0.00352 ( 4) SS BOND : angle 0.46420 ( 8) covalent geometry : bond 0.00468 ( 5245) covalent geometry : angle 0.62506 ( 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 137 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7938 (m-80) cc_final: 0.7480 (m-10) REVERT: H 53 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.8274 (p90) REVERT: H 116 TYR cc_start: 0.8286 (m-80) cc_final: 0.7982 (m-10) REVERT: H 134 SER cc_start: 0.8517 (m) cc_final: 0.7778 (p) REVERT: L 48 LEU cc_start: 0.9026 (mt) cc_final: 0.8802 (mm) REVERT: L 50 TYR cc_start: 0.8289 (p90) cc_final: 0.7891 (p90) REVERT: L 77 SER cc_start: 0.8228 (p) cc_final: 0.7806 (t) outliers start: 27 outliers final: 19 residues processed: 122 average time/residue: 0.1531 time to fit residues: 24.4383 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 : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 137 LEU 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 245 CYS 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.134387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.122871 restraints weight = 10919.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.125322 restraints weight = 6610.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126991 restraints weight = 4399.832| |-----------------------------------------------------------------------------| r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5249 Z= 0.140 Angle : 0.589 7.425 7180 Z= 0.303 Chirality : 0.043 0.156 853 Planarity : 0.004 0.043 923 Dihedral : 4.279 31.137 760 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.71 % Allowed : 21.99 % Favored : 72.30 % 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: 0.32 (0.34), residues: 700 helix: 2.04 (0.33), residues: 248 sheet: -0.14 (0.43), residues: 156 loop : -1.20 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 164 HIS 0.003 0.001 HIS C 1 PHE 0.017 0.002 PHE L 120 TYR 0.022 0.002 TYR L 94 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 257) hydrogen bonds : angle 4.61328 ( 747) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.30509 ( 8) covalent geometry : bond 0.00307 ( 5245) covalent geometry : angle 0.58926 ( 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 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7866 (m-80) cc_final: 0.7404 (m-10) REVERT: H 116 TYR cc_start: 0.8239 (m-80) cc_final: 0.7949 (m-80) REVERT: H 134 SER cc_start: 0.8425 (m) cc_final: 0.7706 (p) REVERT: L 48 LEU cc_start: 0.9040 (mt) cc_final: 0.8811 (mm) REVERT: L 50 TYR cc_start: 0.8273 (p90) cc_final: 0.7896 (p90) REVERT: L 77 SER cc_start: 0.8132 (p) cc_final: 0.7685 (t) REVERT: L 181 LEU cc_start: 0.8746 (tp) cc_final: 0.8528 (tt) REVERT: A 269 LEU cc_start: 0.7112 (mt) cc_final: 0.6841 (mt) outliers start: 27 outliers final: 19 residues processed: 119 average time/residue: 0.1550 time to fit residues: 24.0366 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 59 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.131623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119768 restraints weight = 10693.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.122361 restraints weight = 6301.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124099 restraints weight = 4146.629| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5249 Z= 0.189 Angle : 0.643 9.702 7180 Z= 0.327 Chirality : 0.044 0.240 853 Planarity : 0.005 0.066 923 Dihedral : 4.438 31.939 760 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.50 % Allowed : 23.26 % Favored : 71.25 % 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: 0.11 (0.33), residues: 700 helix: 1.87 (0.34), residues: 246 sheet: -0.25 (0.42), residues: 156 loop : -1.30 (0.38), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 164 HIS 0.004 0.001 HIS C 1 PHE 0.015 0.002 PHE L 211 TYR 0.021 0.002 TYR A 356 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 257) hydrogen bonds : angle 4.69527 ( 747) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.42736 ( 8) covalent geometry : bond 0.00426 ( 5245) covalent geometry : angle 0.64284 ( 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 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7913 (m-80) cc_final: 0.7447 (m-10) REVERT: H 53 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8109 (p90) REVERT: L 48 LEU cc_start: 0.9023 (mt) cc_final: 0.8789 (mm) REVERT: L 50 TYR cc_start: 0.8278 (p90) cc_final: 0.7875 (p90) REVERT: L 77 SER cc_start: 0.8238 (p) cc_final: 0.7776 (t) outliers start: 26 outliers final: 21 residues processed: 118 average time/residue: 0.1501 time to fit residues: 23.2663 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 53 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 172 ASP Chi-restraints excluded: chain L residue 179 SER 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 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: 3.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.0030 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.0270 chunk 6 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5448 ------------------------------------------------------------------------------- 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 = 0.3869 r_free = 0.3869 target = 0.134399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.123123 restraints weight = 10850.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.125515 restraints weight = 6507.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.127165 restraints weight = 4343.849| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5249 Z= 0.135 Angle : 0.608 7.933 7180 Z= 0.307 Chirality : 0.043 0.193 853 Planarity : 0.006 0.117 923 Dihedral : 4.297 28.600 760 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.50 % Allowed : 23.47 % Favored : 71.04 % 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: 2.14 (0.34), residues: 246 sheet: -0.29 (0.42), residues: 164 loop : -1.16 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 262 HIS 0.003 0.001 HIS C 1 PHE 0.012 0.001 PHE L 211 TYR 0.018 0.002 TYR A 356 ARG 0.001 0.000 ARG A 249 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 257) hydrogen bonds : angle 4.52629 ( 747) SS BOND : bond 0.00192 ( 4) SS BOND : angle 0.38609 ( 8) covalent geometry : bond 0.00299 ( 5245) covalent geometry : angle 0.60870 ( 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 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7845 (m-80) cc_final: 0.7402 (m-10) REVERT: H 116 TYR cc_start: 0.8308 (m-80) cc_final: 0.8079 (m-80) REVERT: L 48 LEU cc_start: 0.9048 (mt) cc_final: 0.8826 (mm) REVERT: L 50 TYR cc_start: 0.8265 (p90) cc_final: 0.7853 (p90) REVERT: L 77 SER cc_start: 0.8103 (p) cc_final: 0.7644 (t) REVERT: A 348 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6411 (pp30) REVERT: A 353 ARG cc_start: 0.6465 (ptm-80) cc_final: 0.5804 (ptm160) outliers start: 26 outliers final: 22 residues processed: 119 average time/residue: 0.1717 time to fit residues: 26.5022 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.3272 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.135678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124244 restraints weight = 10880.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126706 restraints weight = 6558.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128369 restraints weight = 4349.438| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5249 Z= 0.116 Angle : 0.593 7.892 7180 Z= 0.297 Chirality : 0.042 0.159 853 Planarity : 0.005 0.088 923 Dihedral : 4.091 24.424 760 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.71 % Allowed : 24.10 % Favored : 70.19 % 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: 0.44 (0.34), residues: 700 helix: 2.30 (0.34), residues: 247 sheet: -0.11 (0.43), residues: 156 loop : -1.25 (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 0.013 0.001 PHE L 211 TYR 0.018 0.001 TYR A 356 ARG 0.004 0.000 ARG L 144 Details of bonding type rmsd hydrogen bonds : bond 0.03399 ( 257) hydrogen bonds : angle 4.34863 ( 747) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.49358 ( 8) covalent geometry : bond 0.00254 ( 5245) covalent geometry : angle 0.59295 ( 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 139 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7805 (m-80) cc_final: 0.7374 (m-10) REVERT: H 116 TYR cc_start: 0.8200 (m-80) cc_final: 0.7962 (m-80) REVERT: H 194 SER cc_start: 0.8029 (t) cc_final: 0.7755 (m) REVERT: L 48 LEU cc_start: 0.9054 (mt) cc_final: 0.8849 (mm) REVERT: L 50 TYR cc_start: 0.8219 (p90) cc_final: 0.7812 (p90) REVERT: L 77 SER cc_start: 0.8070 (p) cc_final: 0.7611 (t) REVERT: A 348 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6330 (pp30) outliers start: 27 outliers final: 23 residues processed: 126 average time/residue: 0.1707 time to fit residues: 28.1157 Evaluate side-chains 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 109 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 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 172 ASP Chi-restraints excluded: chain L residue 179 SER 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 258 LEU Chi-restraints excluded: chain A residue 281 VAL 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: 2.9990 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.0000 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.133858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122043 restraints weight = 10815.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124670 restraints weight = 6330.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126413 restraints weight = 4128.942| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.4022 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= 0.143 Angle : 0.611 8.132 7180 Z= 0.308 Chirality : 0.043 0.172 853 Planarity : 0.005 0.090 923 Dihedral : 4.133 23.901 760 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.86 % Allowed : 24.52 % Favored : 70.61 % 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: 0.40 (0.34), residues: 700 helix: 2.23 (0.34), residues: 247 sheet: -0.08 (0.43), residues: 156 loop : -1.27 (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 0.014 0.001 PHE L 211 TYR 0.017 0.002 TYR A 356 ARG 0.003 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 257) hydrogen bonds : angle 4.38194 ( 747) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.64733 ( 8) covalent geometry : bond 0.00318 ( 5245) covalent geometry : angle 0.61047 ( 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: 23 poor density : 107 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7861 (m-80) cc_final: 0.7389 (m-10) REVERT: L 48 LEU cc_start: 0.9040 (mt) cc_final: 0.8808 (mm) REVERT: L 50 TYR cc_start: 0.8205 (p90) cc_final: 0.7224 (p90) REVERT: L 54 SER cc_start: 0.9326 (m) cc_final: 0.9052 (p) REVERT: L 77 SER cc_start: 0.8132 (p) cc_final: 0.7710 (t) outliers start: 23 outliers final: 22 residues processed: 119 average time/residue: 0.1540 time to fit residues: 24.0047 Evaluate side-chains 127 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.550 ------------------------------------------------------------------------------- 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 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 179 SER 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 258 LEU 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 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: 4.9990 chunk 6 optimal weight: 0.0770 chunk 56 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.6140 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.134101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122332 restraints weight = 10831.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124965 restraints weight = 6316.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126718 restraints weight = 4121.397| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5249 Z= 0.139 Angle : 0.605 7.638 7180 Z= 0.307 Chirality : 0.043 0.165 853 Planarity : 0.005 0.083 923 Dihedral : 4.089 22.074 760 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.29 % Allowed : 23.89 % 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: 0.42 (0.34), residues: 700 helix: 2.26 (0.34), residues: 247 sheet: -0.04 (0.43), residues: 156 loop : -1.29 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 164 HIS 0.003 0.001 HIS C 1 PHE 0.013 0.001 PHE L 211 TYR 0.018 0.002 TYR A 356 ARG 0.002 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 257) hydrogen bonds : angle 4.32636 ( 747) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.48221 ( 8) covalent geometry : bond 0.00312 ( 5245) covalent geometry : angle 0.60501 ( 7172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1889.13 seconds wall clock time: 34 minutes 19.03 seconds (2059.03 seconds total)