Starting phenix.real_space_refine on Wed Sep 17 05:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l3z_62799/09_2025/9l3z_62799.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l3z_62799/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9l3z_62799/09_2025/9l3z_62799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l3z_62799/09_2025/9l3z_62799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l3z_62799/09_2025/9l3z_62799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l3z_62799/09_2025/9l3z_62799.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 9, 'PHE:plan': 14, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'HIS:plan': 4, 'GLN:plan1': 5, 'GLU:plan': 4} 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: 1.39, per 1000 atoms: 0.27 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: 0.43 Conformation dependent library (CDL) restraints added in 179.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 0.65 Time building geometry restraints manager: 0.56 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: 1.510 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.320 Find NCS groups from input model: 0.020 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (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 ARG 0.002 0.000 ARG A 353 TYR 0.015 0.001 TYR L 92 PHE 0.006 0.001 PHE H 35 TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS H 38 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5245) covalent geometry : angle 0.54231 ( 7172) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.36369 ( 8) hydrogen bonds : bond 0.26532 ( 257) hydrogen bonds : angle 8.54911 ( 747) *********************** 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 : 0.194 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: 0.8103 (tp) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.0717 time to fit residues: 11.4312 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 : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.132840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122064 restraints weight = 10749.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124262 restraints weight = 6760.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.125786 restraints weight = 4634.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.126896 restraints weight = 3390.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.127558 restraints weight = 2603.260| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5249 Z= 0.156 Angle : 0.600 8.985 7180 Z= 0.315 Chirality : 0.043 0.159 853 Planarity : 0.005 0.043 923 Dihedral : 4.157 36.228 760 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.02 % Allowed : 16.70 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.34), residues: 700 helix: 1.79 (0.33), residues: 247 sheet: -0.20 (0.44), residues: 157 loop : -1.12 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.023 0.002 TYR L 142 PHE 0.017 0.002 PHE L 120 TRP 0.010 0.001 TRP H 39 HIS 0.003 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 5245) covalent geometry : angle 0.60019 ( 7172) SS BOND : bond 0.00088 ( 4) SS BOND : angle 0.56453 ( 8) hydrogen bonds : bond 0.04832 ( 257) hydrogen bonds : angle 5.23393 ( 747) *********************** 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 126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: L 50 TYR cc_start: 0.8409 (p90) cc_final: 0.7904 (p90) REVERT: L 77 SER cc_start: 0.7970 (p) cc_final: 0.7584 (t) REVERT: L 137 LEU cc_start: 0.8481 (tp) cc_final: 0.8249 (tp) REVERT: L 142 TYR cc_start: 0.6675 (t80) cc_final: 0.6186 (t80) REVERT: A 333 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (tt) REVERT: A 416 THR cc_start: 0.6540 (OUTLIER) cc_final: 0.6275 (t) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.0619 time to fit residues: 9.6220 Evaluate side-chains 110 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 SER 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 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 203 LEU 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 351 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 416 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 22 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.135110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.123104 restraints weight = 10591.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.125673 restraints weight = 6226.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127427 restraints weight = 4111.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128613 restraints weight = 2933.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129470 restraints weight = 2233.061| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5249 Z= 0.164 Angle : 0.579 6.335 7180 Z= 0.305 Chirality : 0.043 0.150 853 Planarity : 0.004 0.043 923 Dihedral : 4.185 36.589 760 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.44 % Allowed : 18.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.34), residues: 700 helix: 1.87 (0.34), residues: 248 sheet: -0.11 (0.44), residues: 156 loop : -1.05 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 249 TYR 0.021 0.002 TYR L 94 PHE 0.012 0.001 PHE A 88 TRP 0.008 0.001 TRP A 164 HIS 0.003 0.001 HIS L 200 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 5245) covalent geometry : angle 0.57912 ( 7172) SS BOND : bond 0.00075 ( 4) SS BOND : angle 0.53752 ( 8) hydrogen bonds : bond 0.04512 ( 257) hydrogen bonds : angle 4.91370 ( 747) *********************** 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 126 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.8018 (m-80) cc_final: 0.7562 (m-10) REVERT: H 116 TYR cc_start: 0.8350 (m-80) cc_final: 0.8143 (m-80) REVERT: H 134 SER cc_start: 0.8486 (m) cc_final: 0.7887 (p) REVERT: L 50 TYR cc_start: 0.8311 (p90) cc_final: 0.7872 (p90) REVERT: L 77 SER cc_start: 0.8125 (p) cc_final: 0.7766 (t) outliers start: 21 outliers final: 16 residues processed: 115 average time/residue: 0.0631 time to fit residues: 9.6894 Evaluate side-chains 115 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 20 SER 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 165 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 203 LEU 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 394 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 4 optimal weight: 0.0970 chunk 25 optimal weight: 0.0010 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 A 121 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120264 restraints weight = 10736.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.122866 restraints weight = 6327.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.124569 restraints weight = 4179.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125820 restraints weight = 3008.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126738 restraints weight = 2284.773| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3013 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= 0.181 Angle : 0.608 9.991 7180 Z= 0.313 Chirality : 0.043 0.161 853 Planarity : 0.005 0.044 923 Dihedral : 4.398 37.089 760 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.71 % Allowed : 21.14 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.34), residues: 700 helix: 1.79 (0.33), residues: 248 sheet: -0.22 (0.43), residues: 158 loop : -1.21 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 137 TYR 0.031 0.002 TYR L 94 PHE 0.012 0.001 PHE A 88 TRP 0.010 0.002 TRP A 164 HIS 0.004 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 5245) covalent geometry : angle 0.60777 ( 7172) SS BOND : bond 0.00403 ( 4) SS BOND : angle 0.45320 ( 8) hydrogen bonds : bond 0.04275 ( 257) hydrogen bonds : angle 4.81363 ( 747) *********************** 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 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7961 (m-80) cc_final: 0.7530 (m-10) REVERT: H 53 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.8170 (p90) REVERT: H 134 SER cc_start: 0.8463 (m) cc_final: 0.7712 (p) REVERT: L 48 LEU cc_start: 0.9037 (mt) cc_final: 0.8816 (mm) REVERT: L 50 TYR cc_start: 0.8302 (p90) cc_final: 0.7872 (p90) REVERT: L 77 SER cc_start: 0.8157 (p) cc_final: 0.7727 (t) outliers start: 27 outliers final: 19 residues processed: 120 average time/residue: 0.0657 time to fit residues: 10.6003 Evaluate side-chains 125 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.187 ------------------------------------------------------------------------------- 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 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 L residue 203 LEU 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 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 39 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 19 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- 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 = 0.134284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122654 restraints weight = 11101.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125086 restraints weight = 6703.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126734 restraints weight = 4491.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127920 restraints weight = 3238.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128677 restraints weight = 2464.413| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5249 Z= 0.136 Angle : 0.587 10.407 7180 Z= 0.296 Chirality : 0.042 0.148 853 Planarity : 0.004 0.043 923 Dihedral : 4.210 32.394 760 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.44 % Allowed : 23.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.34), residues: 700 helix: 2.07 (0.33), residues: 248 sheet: -0.20 (0.43), residues: 156 loop : -1.22 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 70 TYR 0.029 0.002 TYR L 94 PHE 0.013 0.002 PHE L 120 TRP 0.008 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 5245) covalent geometry : angle 0.58729 ( 7172) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.34700 ( 8) hydrogen bonds : bond 0.03882 ( 257) hydrogen bonds : angle 4.61076 ( 747) *********************** 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 128 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7881 (m-80) cc_final: 0.7400 (m-10) REVERT: H 116 TYR cc_start: 0.8168 (m-80) cc_final: 0.7904 (m-80) REVERT: H 134 SER cc_start: 0.8432 (m) cc_final: 0.7720 (p) REVERT: L 48 LEU cc_start: 0.9044 (mt) cc_final: 0.8827 (mm) REVERT: L 50 TYR cc_start: 0.8264 (p90) cc_final: 0.7894 (p90) REVERT: L 77 SER cc_start: 0.8081 (p) cc_final: 0.7605 (t) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.0649 time to fit residues: 10.0295 Evaluate side-chains 121 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 198 VAL Chi-restraints excluded: chain L residue 203 LEU 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 19 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.135105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123515 restraints weight = 11112.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125948 restraints weight = 6676.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127540 restraints weight = 4463.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128762 restraints weight = 3229.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129558 restraints weight = 2439.918| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3435 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= 0.127 Angle : 0.582 10.165 7180 Z= 0.294 Chirality : 0.042 0.149 853 Planarity : 0.004 0.042 923 Dihedral : 4.140 29.551 760 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.92 % Allowed : 21.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.34), residues: 700 helix: 2.16 (0.33), residues: 248 sheet: -0.18 (0.43), residues: 158 loop : -1.24 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 249 TYR 0.029 0.002 TYR L 94 PHE 0.018 0.001 PHE L 120 TRP 0.008 0.001 TRP A 164 HIS 0.003 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5245) covalent geometry : angle 0.58247 ( 7172) SS BOND : bond 0.00624 ( 4) SS BOND : angle 0.30155 ( 8) hydrogen bonds : bond 0.03651 ( 257) hydrogen bonds : angle 4.48618 ( 747) *********************** 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 135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7852 (m-80) cc_final: 0.7408 (m-10) REVERT: H 116 TYR cc_start: 0.8144 (m-80) cc_final: 0.7910 (m-80) REVERT: H 134 SER cc_start: 0.8398 (m) cc_final: 0.7701 (p) REVERT: L 48 LEU cc_start: 0.9047 (mt) cc_final: 0.8814 (mm) REVERT: L 50 TYR cc_start: 0.8224 (p90) cc_final: 0.7830 (p90) REVERT: L 77 SER cc_start: 0.8048 (p) cc_final: 0.7594 (t) outliers start: 28 outliers final: 18 residues processed: 122 average time/residue: 0.0643 time to fit residues: 10.3929 Evaluate side-chains 122 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.132737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120824 restraints weight = 10950.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123396 restraints weight = 6429.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125156 restraints weight = 4235.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126396 restraints weight = 3015.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.127245 restraints weight = 2270.623| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3645 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= 0.165 Angle : 0.623 9.678 7180 Z= 0.314 Chirality : 0.043 0.223 853 Planarity : 0.004 0.043 923 Dihedral : 4.276 29.360 760 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.29 % Allowed : 23.04 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.33), residues: 700 helix: 2.03 (0.33), residues: 248 sheet: -0.23 (0.43), residues: 156 loop : -1.26 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.027 0.002 TYR L 94 PHE 0.012 0.002 PHE L 120 TRP 0.007 0.001 TRP H 105 HIS 0.004 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5245) covalent geometry : angle 0.62325 ( 7172) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.38608 ( 8) hydrogen bonds : bond 0.03964 ( 257) hydrogen bonds : angle 4.56862 ( 747) *********************** 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: 25 poor density : 109 time to evaluate : 0.190 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7900 (m-80) cc_final: 0.7404 (m-10) REVERT: H 134 SER cc_start: 0.8424 (m) cc_final: 0.7788 (p) REVERT: L 48 LEU cc_start: 0.9026 (mt) cc_final: 0.8781 (mm) REVERT: L 50 TYR cc_start: 0.8260 (p90) cc_final: 0.7829 (p90) REVERT: L 77 SER cc_start: 0.8180 (p) cc_final: 0.7710 (t) REVERT: L 168 GLN cc_start: 0.7513 (mm110) cc_final: 0.7248 (mm110) outliers start: 25 outliers final: 21 residues processed: 121 average time/residue: 0.0602 time to fit residues: 9.7629 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.0570 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.134462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122541 restraints weight = 10881.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.125182 restraints weight = 6322.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.126969 restraints weight = 4128.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.128212 restraints weight = 2909.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.129042 restraints weight = 2175.934| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3767 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= 0.128 Angle : 0.601 9.749 7180 Z= 0.302 Chirality : 0.043 0.177 853 Planarity : 0.005 0.065 923 Dihedral : 4.138 26.054 760 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.86 % Allowed : 23.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.34), residues: 700 helix: 2.29 (0.34), residues: 247 sheet: -0.20 (0.42), residues: 156 loop : -1.23 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 353 TYR 0.022 0.002 TYR L 94 PHE 0.012 0.001 PHE A 88 TRP 0.009 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 5245) covalent geometry : angle 0.60102 ( 7172) SS BOND : bond 0.00240 ( 4) SS BOND : angle 0.29591 ( 8) hydrogen bonds : bond 0.03597 ( 257) hydrogen bonds : angle 4.42778 ( 747) *********************** 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 134 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7886 (m-80) cc_final: 0.7403 (m-10) REVERT: H 116 TYR cc_start: 0.8305 (m-80) cc_final: 0.7948 (m-10) REVERT: H 134 SER cc_start: 0.8406 (m) cc_final: 0.7788 (p) REVERT: L 48 LEU cc_start: 0.9032 (mt) cc_final: 0.8794 (mm) REVERT: L 50 TYR cc_start: 0.8215 (p90) cc_final: 0.7779 (p90) REVERT: L 77 SER cc_start: 0.8135 (p) cc_final: 0.7683 (t) REVERT: L 168 GLN cc_start: 0.7419 (mm110) cc_final: 0.7086 (mm110) outliers start: 23 outliers final: 21 residues processed: 122 average time/residue: 0.0649 time to fit residues: 10.5386 Evaluate side-chains 130 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 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 265 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 6 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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** 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 = 0.136524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.124882 restraints weight = 10816.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.127452 restraints weight = 6353.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129197 restraints weight = 4167.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130387 restraints weight = 2936.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131145 restraints weight = 2202.952| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5249 Z= 0.114 Angle : 0.597 9.583 7180 Z= 0.295 Chirality : 0.042 0.161 853 Planarity : 0.005 0.081 923 Dihedral : 4.005 22.151 760 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.65 % Allowed : 25.37 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.34), residues: 700 helix: 2.43 (0.33), residues: 247 sheet: -0.12 (0.43), residues: 156 loop : -1.24 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.021 0.001 TYR L 94 PHE 0.011 0.001 PHE A 88 TRP 0.007 0.001 TRP A 164 HIS 0.002 0.001 HIS C 1 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 5245) covalent geometry : angle 0.59724 ( 7172) SS BOND : bond 0.00304 ( 4) SS BOND : angle 0.30963 ( 8) hydrogen bonds : bond 0.03363 ( 257) hydrogen bonds : angle 4.28970 ( 747) *********************** 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 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7849 (m-80) cc_final: 0.7381 (m-10) REVERT: H 116 TYR cc_start: 0.8215 (m-80) cc_final: 0.7967 (m-80) REVERT: H 134 SER cc_start: 0.8332 (m) cc_final: 0.7710 (p) REVERT: H 194 SER cc_start: 0.8048 (t) cc_final: 0.7767 (m) REVERT: L 48 LEU cc_start: 0.9048 (mt) cc_final: 0.8822 (mm) REVERT: L 50 TYR cc_start: 0.8209 (p90) cc_final: 0.7784 (p90) REVERT: L 77 SER cc_start: 0.8069 (p) cc_final: 0.7626 (t) REVERT: L 142 TYR cc_start: 0.7038 (t80) cc_final: 0.6485 (t80) REVERT: L 168 GLN cc_start: 0.7338 (mm110) cc_final: 0.7055 (mm110) REVERT: A 353 ARG cc_start: 0.6009 (ptm-80) cc_final: 0.5589 (ptm-80) outliers start: 22 outliers final: 19 residues processed: 123 average time/residue: 0.0578 time to fit residues: 9.4952 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 265 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 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.136353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.124632 restraints weight = 11060.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.127276 restraints weight = 6472.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129005 restraints weight = 4217.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130162 restraints weight = 2969.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131108 restraints weight = 2232.209| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5249 Z= 0.123 Angle : 0.611 9.537 7180 Z= 0.303 Chirality : 0.042 0.151 853 Planarity : 0.004 0.059 923 Dihedral : 3.981 21.053 760 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 4.44 % Allowed : 25.16 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.34), residues: 700 helix: 2.23 (0.33), residues: 247 sheet: -0.07 (0.43), residues: 156 loop : -1.28 (0.38), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.021 0.002 TYR L 94 PHE 0.011 0.001 PHE A 88 TRP 0.007 0.001 TRP A 262 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5245) covalent geometry : angle 0.61082 ( 7172) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.47731 ( 8) hydrogen bonds : bond 0.03405 ( 257) hydrogen bonds : angle 4.25913 ( 747) ********************** 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 135 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: H 35 PHE cc_start: 0.7850 (m-80) cc_final: 0.7379 (m-10) REVERT: H 86 MET cc_start: 0.8241 (mmm) cc_final: 0.8008 (mmt) REVERT: H 116 TYR cc_start: 0.8226 (m-80) cc_final: 0.7900 (m-10) REVERT: H 134 SER cc_start: 0.8293 (m) cc_final: 0.7792 (p) REVERT: H 194 SER cc_start: 0.8078 (t) cc_final: 0.7794 (m) REVERT: L 48 LEU cc_start: 0.9057 (mt) cc_final: 0.8826 (mm) REVERT: L 50 TYR cc_start: 0.8195 (p90) cc_final: 0.7177 (p90) REVERT: L 54 SER cc_start: 0.9294 (m) cc_final: 0.9009 (p) REVERT: L 77 SER cc_start: 0.8047 (p) cc_final: 0.7594 (t) REVERT: L 168 GLN cc_start: 0.7348 (mm110) cc_final: 0.7044 (mm110) REVERT: A 348 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6362 (pp30) REVERT: A 353 ARG cc_start: 0.6060 (ptm-80) cc_final: 0.5604 (ptm-80) outliers start: 21 outliers final: 20 residues processed: 125 average time/residue: 0.0618 time to fit residues: 10.3936 Evaluate side-chains 133 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 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 265 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 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 17 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 35 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.135633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123868 restraints weight = 10983.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126550 restraints weight = 6383.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.128328 restraints weight = 4145.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129588 restraints weight = 2909.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.130411 restraints weight = 2161.592| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.4059 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= 0.128 Angle : 0.608 9.394 7180 Z= 0.301 Chirality : 0.042 0.156 853 Planarity : 0.004 0.049 923 Dihedral : 3.953 20.221 760 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.65 % Allowed : 24.95 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.34), residues: 700 helix: 2.18 (0.33), residues: 253 sheet: -0.06 (0.43), residues: 156 loop : -1.24 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 353 TYR 0.021 0.002 TYR L 94 PHE 0.011 0.001 PHE A 88 TRP 0.006 0.001 TRP H 105 HIS 0.002 0.001 HIS A 121 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5245) covalent geometry : angle 0.60728 ( 7172) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.77981 ( 8) hydrogen bonds : bond 0.03409 ( 257) hydrogen bonds : angle 4.24374 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 953.36 seconds wall clock time: 17 minutes 12.13 seconds (1032.13 seconds total)