Starting phenix.real_space_refine on Thu Jul 2 07:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.map" model { file = "/net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cp5_45800/07_2026/9cp5_45800.cif" } resolution = 3.51 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= -0.003 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 1 4.86 5 C 4842 2.51 5 N 1182 2.21 5 O 1367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7450 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4253 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 512} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1599 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1597 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CL': 1} Chain breaks: 1 Time building chain proxies: 1.45, per 1000 atoms: 0.19 Number of scatterers: 7450 At special positions: 0 Unit cell: (78.934, 85.404, 151.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 58 16.00 O 1367 8.00 N 1182 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 171 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " 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: 0.54 Conformation dependent library (CDL) restraints added in 438.1 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1780 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 45.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 57 through 68 removed outlier: 3.835A pdb=" N GLU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 74 through 83 removed outlier: 3.697A pdb=" N TYR A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 99 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.700A pdb=" N VAL A 103 " --> pdb=" O CYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.908A pdb=" N TYR A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 removed outlier: 4.222A pdb=" N PHE A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.686A pdb=" N ALA A 169 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 170 " --> pdb=" O PRO A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 170' Processing helix chain 'A' and resid 201 through 211 removed outlier: 3.604A pdb=" N GLU A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 245 Processing helix chain 'A' and resid 259 through 275 removed outlier: 3.643A pdb=" N THR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 3.732A pdb=" N GLY A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.384A pdb=" N TRP A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 removed outlier: 4.152A pdb=" N ALA A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.836A pdb=" N ASP A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.659A pdb=" N GLU A 369 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 370 " --> pdb=" O ILE A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 366 through 370' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 386 Processing helix chain 'A' and resid 391 through 426 removed outlier: 3.680A pdb=" N TRP A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.971A pdb=" N PHE A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 426 through 431' Processing helix chain 'A' and resid 435 through 452 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 458 through 470 removed outlier: 4.129A pdb=" N ILE A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 490 Processing helix chain 'A' and resid 492 through 505 Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 547 through 563 Processing helix chain 'A' and resid 563 through 576 Processing helix chain 'A' and resid 579 through 589 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.638A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.672A pdb=" N ASP L 83 " --> pdb=" O GLU L 80 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA L 84 " --> pdb=" O ALA L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'L' and resid 122 through 128 removed outlier: 3.651A pdb=" N LEU L 126 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER L 128 " --> pdb=" O GLN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.576A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.240A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.589A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR H 181 " --> pdb=" O GLY H 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.589A pdb=" N SER H 126 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR H 181 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR H 182 " --> pdb=" O VAL H 175 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL H 175 " --> pdb=" O THR H 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.738A pdb=" N THR H 159 " --> pdb=" O ASN H 202 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN H 202 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.790A pdb=" N VAL L 19 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR L 72 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.818A pdb=" N MET L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 117 through 119 removed outlier: 6.302A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 154 through 156 removed outlier: 3.851A pdb=" N TRP L 149 " --> pdb=" O ARG L 156 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1110 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: 0.99 Time building geometry restraints manager: 0.77 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: 2252 1.34 - 1.46: 2025 1.46 - 1.58: 3300 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 7659 Sorted by residual: bond pdb=" C PRO A 508 " pdb=" N PRO A 509 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.66e+00 bond pdb=" N ASN L 213 " pdb=" CA ASN L 213 " ideal model delta sigma weight residual 1.458 1.482 -0.024 1.90e-02 2.77e+03 1.61e+00 bond pdb=" C ILE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.336 1.350 -0.015 1.23e-02 6.61e+03 1.43e+00 bond pdb=" CA ILE A 543 " pdb=" CB ILE A 543 " ideal model delta sigma weight residual 1.540 1.556 -0.016 1.36e-02 5.41e+03 1.40e+00 bond pdb=" C SER A 392 " pdb=" N PRO A 393 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.28e-02 6.10e+03 1.28e+00 ... (remaining 7654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10073 1.68 - 3.36: 306 3.36 - 5.04: 37 5.04 - 6.73: 14 6.73 - 8.41: 14 Bond angle restraints: 10444 Sorted by residual: angle pdb=" C SER L 51 " pdb=" N THR L 52 " pdb=" CA THR L 52 " ideal model delta sigma weight residual 121.54 129.56 -8.02 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C TYR A 191 " pdb=" N SER A 192 " pdb=" CA SER A 192 " ideal model delta sigma weight residual 121.54 129.29 -7.75 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ARG L 212 " pdb=" N ASN L 213 " pdb=" CA ASN L 213 " ideal model delta sigma weight residual 121.70 128.44 -6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C PRO A 509 " pdb=" N SER A 510 " pdb=" CA SER A 510 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.27e+01 angle pdb=" C GLY A 578 " pdb=" N THR A 579 " pdb=" CA THR A 579 " ideal model delta sigma weight residual 121.54 128.22 -6.68 1.91e+00 2.74e-01 1.22e+01 ... (remaining 10439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4016 17.95 - 35.90: 331 35.90 - 53.85: 68 53.85 - 71.80: 8 71.80 - 89.75: 11 Dihedral angle restraints: 4434 sinusoidal: 1641 harmonic: 2793 Sorted by residual: dihedral pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " pdb=" SG CYS A 180 " pdb=" CB CYS A 180 " ideal model delta sinusoidal sigma weight residual -86.00 -162.42 76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA MET A 517 " pdb=" C MET A 517 " pdb=" N ILE A 518 " pdb=" CA ILE A 518 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA THR A 579 " pdb=" C THR A 579 " pdb=" N LEU A 580 " pdb=" CA LEU A 580 " ideal model delta harmonic sigma weight residual -180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 825 0.044 - 0.088: 258 0.088 - 0.132: 79 0.132 - 0.176: 12 0.176 - 0.220: 4 Chirality restraints: 1178 Sorted by residual: chirality pdb=" CB ILE A 543 " pdb=" CA ILE A 543 " pdb=" CG1 ILE A 543 " pdb=" CG2 ILE A 543 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CG LEU A 455 " pdb=" CB LEU A 455 " pdb=" CD1 LEU A 455 " pdb=" CD2 LEU A 455 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA TYR A 382 " pdb=" N TYR A 382 " pdb=" C TYR A 382 " pdb=" CB TYR A 382 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1175 not shown) Planarity restraints: 1292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 350 " -0.014 2.00e-02 2.50e+03 1.55e-02 4.19e+00 pdb=" CG PHE A 350 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 350 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 350 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 350 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 350 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 350 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 207 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.53e+00 pdb=" C TRP A 207 " -0.033 2.00e-02 2.50e+03 pdb=" O TRP A 207 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 208 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 365 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 366 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 366 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 366 " -0.024 5.00e-02 4.00e+02 ... (remaining 1289 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1371 2.77 - 3.30: 6884 3.30 - 3.84: 12734 3.84 - 4.37: 14081 4.37 - 4.90: 25096 Nonbonded interactions: 60166 Sorted by model distance: nonbonded pdb=" OE1 GLU L 106 " pdb=" OH TYR L 174 " model vdw 2.238 3.040 nonbonded pdb=" O CYS A 98 " pdb=" OG1 THR A 520 " model vdw 2.282 3.040 nonbonded pdb=" O SER H 140 " pdb=" OG SER H 191 " model vdw 2.312 3.040 nonbonded pdb=" ND2 ASN A 83 " pdb=" OD2 ASP A 301 " model vdw 2.317 3.120 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.318 3.040 ... (remaining 60161 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: 1.230 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.120 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 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 0.050 7664 Z= 0.166 Angle : 0.734 8.408 10454 Z= 0.381 Chirality : 0.048 0.220 1178 Planarity : 0.005 0.042 1292 Dihedral : 14.363 89.746 2639 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -1.74 (0.25), residues: 958 helix: -0.55 (0.24), residues: 380 sheet: -1.17 (0.39), residues: 182 loop : -1.62 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 44 TYR 0.020 0.001 TYR A 382 PHE 0.036 0.002 PHE A 350 TRP 0.016 0.001 TRP A 549 HIS 0.003 0.001 HIS A 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 ( 7659) covalent geometry : angle 0.73350 / 0.38 (10444) SS BOND : bond 0.00205 / 0.09 ( 5) SS BOND : angle 1.16908 / 0.62 ( 10) hydrogen bonds : bond 0.19299 / 12.99 ( 375) hydrogen bonds : angle 8.06078 / 5.83 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 66 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7309 (mm-30) REVERT: A 97 ILE cc_start: 0.8066 (mm) cc_final: 0.7659 (pt) REVERT: A 184 GLN cc_start: 0.7409 (mm110) cc_final: 0.7094 (mm-40) REVERT: A 220 HIS cc_start: 0.7678 (m-70) cc_final: 0.7340 (m-70) REVERT: A 226 TRP cc_start: 0.6837 (m100) cc_final: 0.6196 (p-90) REVERT: A 230 LEU cc_start: 0.8077 (mm) cc_final: 0.7839 (tp) REVERT: A 299 TRP cc_start: 0.8308 (m100) cc_final: 0.7745 (m100) REVERT: A 335 ILE cc_start: 0.7893 (mm) cc_final: 0.7473 (tp) REVERT: A 336 MET cc_start: 0.7985 (ptt) cc_final: 0.7734 (ptp) REVERT: A 339 CYS cc_start: 0.7004 (t) cc_final: 0.6361 (m) REVERT: A 389 MET cc_start: 0.7500 (mmm) cc_final: 0.6993 (mtt) REVERT: A 416 GLU cc_start: 0.8490 (tt0) cc_final: 0.8064 (tp30) REVERT: A 444 SER cc_start: 0.8679 (m) cc_final: 0.8461 (p) REVERT: A 457 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6944 (tt0) REVERT: A 518 ILE cc_start: 0.8435 (pt) cc_final: 0.8199 (tp) REVERT: A 551 TYR cc_start: 0.7117 (m-10) cc_final: 0.6889 (m-10) REVERT: A 557 MET cc_start: 0.7669 (ppp) cc_final: 0.6739 (ppp) REVERT: H 7 SER cc_start: 0.7673 (t) cc_final: 0.7446 (p) REVERT: H 13 LYS cc_start: 0.8789 (mptt) cc_final: 0.8504 (mptt) REVERT: H 116 THR cc_start: 0.8533 (m) cc_final: 0.8322 (p) REVERT: L 13 THR cc_start: 0.8634 (p) cc_final: 0.8252 (p) REVERT: L 50 TYR cc_start: 0.9116 (p90) cc_final: 0.8725 (p90) REVERT: L 107 MET cc_start: 0.7964 (mmm) cc_final: 0.7459 (mmt) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.0842 time to fit residues: 25.3612 Evaluate side-chains 145 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN A 160 ASN L 39 GLN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.178282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145357 restraints weight = 10746.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.148870 restraints weight = 6461.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.151266 restraints weight = 4657.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.152789 restraints weight = 3737.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.153716 restraints weight = 3242.567| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7664 Z= 0.148 Angle : 0.625 5.999 10454 Z= 0.325 Chirality : 0.043 0.194 1178 Planarity : 0.004 0.039 1292 Dihedral : 4.243 18.055 1039 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.49 % Allowed : 12.50 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.98 (0.27), residues: 958 helix: 0.35 (0.26), residues: 388 sheet: -0.84 (0.40), residues: 172 loop : -1.50 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 123 TYR 0.017 0.002 TYR H 151 PHE 0.019 0.002 PHE A 350 TRP 0.032 0.001 TRP A 244 HIS 0.007 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7659) covalent geometry : angle 0.62452 / 0.33 (10444) SS BOND : bond 0.00224 / 0.12 ( 5) SS BOND : angle 0.80063 / 0.45 ( 10) hydrogen bonds : bond 0.04668 / 3.23 ( 375) hydrogen bonds : angle 5.76678 / 4.17 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8438 (mm) cc_final: 0.8218 (mt) REVERT: A 226 TRP cc_start: 0.6821 (m100) cc_final: 0.6562 (p-90) REVERT: A 299 TRP cc_start: 0.7921 (m100) cc_final: 0.7687 (m100) REVERT: A 335 ILE cc_start: 0.7830 (mm) cc_final: 0.7589 (tp) REVERT: A 557 MET cc_start: 0.7382 (ppp) cc_final: 0.6876 (ppp) REVERT: H 13 LYS cc_start: 0.8734 (mptt) cc_final: 0.8486 (tppt) REVERT: H 32 TYR cc_start: 0.7255 (m-10) cc_final: 0.6903 (m-10) REVERT: H 151 TYR cc_start: 0.7910 (p90) cc_final: 0.7698 (p90) REVERT: L 1 GLU cc_start: 0.7576 (tp30) cc_final: 0.6954 (tp30) REVERT: L 176 MET cc_start: 0.5793 (tpt) cc_final: 0.5427 (tpt) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.0789 time to fit residues: 17.4438 Evaluate side-chains 134 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 ASN H 103 GLN L 2 ASN L 162 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.177746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144549 restraints weight = 10698.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148131 restraints weight = 6488.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.150466 restraints weight = 4689.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.151982 restraints weight = 3793.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.152829 restraints weight = 3309.575| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7664 Z= 0.132 Angle : 0.593 6.799 10454 Z= 0.303 Chirality : 0.043 0.195 1178 Planarity : 0.004 0.037 1292 Dihedral : 4.170 18.203 1039 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.23 % Allowed : 15.47 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.63 (0.27), residues: 958 helix: 0.59 (0.26), residues: 391 sheet: -0.55 (0.39), residues: 182 loop : -1.34 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 495 TYR 0.014 0.001 TYR H 151 PHE 0.016 0.001 PHE H 29 TRP 0.024 0.001 TRP L 164 HIS 0.004 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7659) covalent geometry : angle 0.59232 / 0.30 (10444) SS BOND : bond 0.00213 / 0.12 ( 5) SS BOND : angle 0.78421 / 0.43 ( 10) hydrogen bonds : bond 0.04255 / 2.95 ( 375) hydrogen bonds : angle 5.35036 / 3.84 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6074 (t80) REVERT: A 97 ILE cc_start: 0.8621 (mm) cc_final: 0.8352 (mt) REVERT: A 226 TRP cc_start: 0.6910 (m100) cc_final: 0.6525 (p-90) REVERT: A 244 TRP cc_start: 0.7259 (t60) cc_final: 0.6908 (t60) REVERT: A 299 TRP cc_start: 0.7941 (m100) cc_final: 0.7619 (m100) REVERT: A 336 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7342 (ptp) REVERT: A 557 MET cc_start: 0.7380 (ppp) cc_final: 0.7044 (ppp) REVERT: A 574 TRP cc_start: 0.6386 (t-100) cc_final: 0.6186 (t-100) REVERT: H 13 LYS cc_start: 0.8749 (mptt) cc_final: 0.8543 (tppt) REVERT: H 151 TYR cc_start: 0.7961 (p90) cc_final: 0.7428 (p90) REVERT: L 2 ASN cc_start: 0.7864 (m110) cc_final: 0.7253 (m-40) REVERT: L 50 TYR cc_start: 0.9007 (p90) cc_final: 0.8801 (p90) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 0.0734 time to fit residues: 14.2766 Evaluate side-chains 127 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 83 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.186625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.148647 restraints weight = 11894.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.153041 restraints weight = 6376.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.155861 restraints weight = 4381.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.157342 restraints weight = 3481.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.158640 restraints weight = 3056.752| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7664 Z= 0.137 Angle : 0.583 6.392 10454 Z= 0.298 Chirality : 0.042 0.161 1178 Planarity : 0.004 0.038 1292 Dihedral : 4.108 17.626 1039 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.98 % Allowed : 16.83 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.42 (0.28), residues: 958 helix: 0.77 (0.26), residues: 392 sheet: -0.42 (0.39), residues: 182 loop : -1.25 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 292 TYR 0.015 0.001 TYR L 141 PHE 0.010 0.001 PHE A 358 TRP 0.030 0.001 TRP L 164 HIS 0.005 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7659) covalent geometry : angle 0.58251 / 0.30 (10444) SS BOND : bond 0.00223 / 0.13 ( 5) SS BOND : angle 0.76993 / 0.42 ( 10) hydrogen bonds : bond 0.03888 / 2.68 ( 375) hydrogen bonds : angle 5.14751 / 3.67 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 97 ILE cc_start: 0.8527 (mm) cc_final: 0.8219 (mt) REVERT: A 226 TRP cc_start: 0.7063 (m100) cc_final: 0.6495 (p-90) REVERT: A 299 TRP cc_start: 0.8094 (m100) cc_final: 0.7691 (m100) REVERT: A 314 LEU cc_start: 0.7261 (mt) cc_final: 0.7049 (mt) REVERT: A 339 CYS cc_start: 0.7573 (t) cc_final: 0.6879 (m) REVERT: A 425 MET cc_start: 0.7422 (mtp) cc_final: 0.7213 (mtp) REVERT: A 574 TRP cc_start: 0.6392 (t-100) cc_final: 0.6189 (t-100) REVERT: H 151 TYR cc_start: 0.7973 (p90) cc_final: 0.7476 (p90) REVERT: L 2 ASN cc_start: 0.8120 (m110) cc_final: 0.7591 (m-40) REVERT: L 107 MET cc_start: 0.7807 (mmm) cc_final: 0.7461 (mmt) outliers start: 16 outliers final: 11 residues processed: 143 average time/residue: 0.0771 time to fit residues: 14.9693 Evaluate side-chains 132 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.185829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147600 restraints weight = 11706.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.151896 restraints weight = 6354.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.154689 restraints weight = 4413.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.156153 restraints weight = 3537.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.157447 restraints weight = 3113.837| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7664 Z= 0.140 Angle : 0.587 6.551 10454 Z= 0.299 Chirality : 0.042 0.149 1178 Planarity : 0.004 0.058 1292 Dihedral : 4.089 16.716 1039 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.09 % Allowed : 17.57 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.26 (0.28), residues: 958 helix: 0.89 (0.27), residues: 387 sheet: -0.30 (0.39), residues: 181 loop : -1.14 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.013 0.001 TYR A 146 PHE 0.011 0.001 PHE A 358 TRP 0.032 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 7659) covalent geometry : angle 0.58658 / 0.30 (10444) SS BOND : bond 0.00229 / 0.13 ( 5) SS BOND : angle 0.84248 / 0.47 ( 10) hydrogen bonds : bond 0.03904 / 2.69 ( 375) hydrogen bonds : angle 5.09248 / 3.63 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.6496 (t80) REVERT: A 97 ILE cc_start: 0.8527 (mm) cc_final: 0.8190 (mt) REVERT: A 226 TRP cc_start: 0.6989 (m100) cc_final: 0.6510 (p-90) REVERT: A 299 TRP cc_start: 0.8098 (m100) cc_final: 0.7663 (m100) REVERT: A 336 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.6993 (mmt) REVERT: A 339 CYS cc_start: 0.7590 (t) cc_final: 0.6839 (m) REVERT: A 443 LEU cc_start: 0.8641 (tp) cc_final: 0.8414 (tp) REVERT: A 464 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8444 (tp-100) REVERT: H 94 TYR cc_start: 0.8685 (m-80) cc_final: 0.8304 (m-80) REVERT: H 151 TYR cc_start: 0.8042 (p90) cc_final: 0.7534 (p90) REVERT: L 2 ASN cc_start: 0.8167 (m110) cc_final: 0.7593 (m-40) REVERT: L 150 LYS cc_start: 0.5335 (mttt) cc_final: 0.5050 (mttp) REVERT: L 164 TRP cc_start: 0.7769 (m-90) cc_final: 0.7435 (m-90) outliers start: 25 outliers final: 17 residues processed: 143 average time/residue: 0.0775 time to fit residues: 15.0535 Evaluate side-chains 139 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.185731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.147744 restraints weight = 11657.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.151970 restraints weight = 6312.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.154706 restraints weight = 4397.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.156451 restraints weight = 3524.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.157227 restraints weight = 3065.546| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7664 Z= 0.141 Angle : 0.598 7.083 10454 Z= 0.301 Chirality : 0.042 0.136 1178 Planarity : 0.004 0.047 1292 Dihedral : 4.048 15.776 1039 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.48 % Allowed : 19.18 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.20 (0.28), residues: 958 helix: 0.96 (0.27), residues: 387 sheet: -0.24 (0.39), residues: 179 loop : -1.14 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 292 TYR 0.012 0.001 TYR A 544 PHE 0.012 0.001 PHE A 260 TRP 0.023 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7659) covalent geometry : angle 0.59726 / 0.30 (10444) SS BOND : bond 0.00249 / 0.14 ( 5) SS BOND : angle 0.82199 / 0.46 ( 10) hydrogen bonds : bond 0.03872 / 2.68 ( 375) hydrogen bonds : angle 5.04500 / 3.59 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.6522 (t80) REVERT: A 97 ILE cc_start: 0.8526 (mm) cc_final: 0.8186 (mt) REVERT: A 226 TRP cc_start: 0.7045 (m100) cc_final: 0.6525 (p-90) REVERT: A 299 TRP cc_start: 0.8133 (m100) cc_final: 0.7681 (m100) REVERT: A 339 CYS cc_start: 0.7564 (t) cc_final: 0.6862 (m) REVERT: A 443 LEU cc_start: 0.8690 (tp) cc_final: 0.8482 (tp) REVERT: H 94 TYR cc_start: 0.8700 (m-80) cc_final: 0.8293 (m-80) REVERT: L 53 SER cc_start: 0.8237 (m) cc_final: 0.8009 (p) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.0771 time to fit residues: 14.4275 Evaluate side-chains 131 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.183877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.146226 restraints weight = 11754.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.150353 restraints weight = 6312.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.153047 restraints weight = 4380.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.154753 restraints weight = 3509.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.155333 restraints weight = 3054.105| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7664 Z= 0.152 Angle : 0.603 7.304 10454 Z= 0.305 Chirality : 0.042 0.128 1178 Planarity : 0.004 0.042 1292 Dihedral : 4.094 15.942 1039 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.22 % Allowed : 18.94 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.20 (0.28), residues: 958 helix: 0.97 (0.27), residues: 387 sheet: -0.40 (0.39), residues: 187 loop : -1.06 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 87 TYR 0.013 0.001 TYR A 551 PHE 0.023 0.001 PHE A 399 TRP 0.033 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7659) covalent geometry : angle 0.60302 / 0.31 (10444) SS BOND : bond 0.00252 / 0.14 ( 5) SS BOND : angle 0.82367 / 0.45 ( 10) hydrogen bonds : bond 0.03938 / 2.74 ( 375) hydrogen bonds : angle 5.03234 / 3.59 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6538 (t80) REVERT: A 97 ILE cc_start: 0.8569 (mm) cc_final: 0.8224 (mt) REVERT: A 121 CYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8439 (p) REVERT: A 226 TRP cc_start: 0.7106 (m100) cc_final: 0.6610 (p-90) REVERT: A 299 TRP cc_start: 0.8182 (m100) cc_final: 0.7710 (m100) REVERT: A 339 CYS cc_start: 0.7576 (t) cc_final: 0.6930 (m) REVERT: A 464 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8462 (tp-100) REVERT: A 503 MET cc_start: 0.7756 (mtp) cc_final: 0.7449 (ttt) REVERT: A 517 MET cc_start: 0.7564 (mmm) cc_final: 0.7248 (mmm) REVERT: H 94 TYR cc_start: 0.8730 (m-80) cc_final: 0.8311 (m-80) REVERT: L 53 SER cc_start: 0.8301 (m) cc_final: 0.8062 (p) REVERT: L 167 GLN cc_start: 0.7503 (mm-40) cc_final: 0.7125 (tp40) outliers start: 26 outliers final: 18 residues processed: 147 average time/residue: 0.0851 time to fit residues: 17.1532 Evaluate side-chains 143 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 81 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN L 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.184634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.146922 restraints weight = 11897.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.151244 restraints weight = 6343.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154043 restraints weight = 4368.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.155472 restraints weight = 3477.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156728 restraints weight = 3060.539| |-----------------------------------------------------------------------------| r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7664 Z= 0.141 Angle : 0.607 7.402 10454 Z= 0.309 Chirality : 0.042 0.123 1178 Planarity : 0.004 0.040 1292 Dihedral : 4.113 15.894 1039 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.35 % Allowed : 20.30 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.18 (0.28), residues: 958 helix: 1.01 (0.27), residues: 387 sheet: -0.43 (0.39), residues: 187 loop : -1.06 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.019 0.001 TYR A 310 PHE 0.016 0.001 PHE A 399 TRP 0.042 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7659) covalent geometry : angle 0.60623 / 0.31 (10444) SS BOND : bond 0.00308 / 0.17 ( 5) SS BOND : angle 1.12187 / 0.62 ( 10) hydrogen bonds : bond 0.03879 / 2.70 ( 375) hydrogen bonds : angle 5.01587 / 3.56 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.286 Fit side-chains REVERT: A 78 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.6590 (t80) REVERT: A 97 ILE cc_start: 0.8557 (mm) cc_final: 0.8258 (mt) REVERT: A 121 CYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 226 TRP cc_start: 0.7084 (m100) cc_final: 0.6665 (p-90) REVERT: A 299 TRP cc_start: 0.8052 (m100) cc_final: 0.7673 (m100) REVERT: A 332 ARG cc_start: 0.5797 (tpp-160) cc_final: 0.4955 (mmt180) REVERT: A 335 ILE cc_start: 0.7767 (mm) cc_final: 0.7456 (tp) REVERT: A 339 CYS cc_start: 0.7475 (t) cc_final: 0.6937 (m) REVERT: A 426 TYR cc_start: 0.7413 (m-10) cc_final: 0.7129 (m-80) REVERT: A 464 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8185 (tp40) REVERT: A 517 MET cc_start: 0.7595 (mmm) cc_final: 0.7258 (mmm) REVERT: H 94 TYR cc_start: 0.8735 (m-80) cc_final: 0.8332 (m-80) REVERT: L 53 SER cc_start: 0.8185 (m) cc_final: 0.7982 (p) REVERT: L 167 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7118 (tp40) outliers start: 19 outliers final: 15 residues processed: 144 average time/residue: 0.0796 time to fit residues: 15.6878 Evaluate side-chains 141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.0040 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 464 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.183120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145582 restraints weight = 11604.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149821 restraints weight = 6263.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.152537 restraints weight = 4345.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.154218 restraints weight = 3477.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.155264 restraints weight = 3033.770| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7664 Z= 0.157 Angle : 0.632 9.110 10454 Z= 0.320 Chirality : 0.043 0.133 1178 Planarity : 0.004 0.039 1292 Dihedral : 4.152 18.487 1039 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.85 % Allowed : 20.17 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.19 (0.28), residues: 958 helix: 0.99 (0.27), residues: 387 sheet: -0.46 (0.38), residues: 187 loop : -1.04 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 98 TYR 0.022 0.002 TYR A 551 PHE 0.017 0.001 PHE A 466 TRP 0.056 0.002 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 7659) covalent geometry : angle 0.63102 / 0.32 (10444) SS BOND : bond 0.00271 / 0.17 ( 5) SS BOND : angle 1.12725 / 0.62 ( 10) hydrogen bonds : bond 0.03974 / 2.78 ( 375) hydrogen bonds : angle 5.04570 / 3.59 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.202 Fit side-chains REVERT: A 78 TYR cc_start: 0.7805 (OUTLIER) cc_final: 0.6593 (t80) REVERT: A 97 ILE cc_start: 0.8559 (mm) cc_final: 0.8262 (mt) REVERT: A 121 CYS cc_start: 0.8707 (OUTLIER) cc_final: 0.7765 (p) REVERT: A 226 TRP cc_start: 0.7120 (m100) cc_final: 0.6698 (p-90) REVERT: A 299 TRP cc_start: 0.8062 (m100) cc_final: 0.7703 (m100) REVERT: A 332 ARG cc_start: 0.5920 (tpp-160) cc_final: 0.5078 (mmt180) REVERT: A 335 ILE cc_start: 0.7953 (mm) cc_final: 0.7561 (tp) REVERT: A 339 CYS cc_start: 0.7534 (t) cc_final: 0.6737 (m) REVERT: A 411 GLN cc_start: 0.8224 (tp40) cc_final: 0.7571 (tp-100) REVERT: A 517 MET cc_start: 0.7571 (mmm) cc_final: 0.7227 (mmm) REVERT: L 80 GLU cc_start: 0.7379 (mp0) cc_final: 0.7170 (mp0) REVERT: L 167 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7164 (tp40) REVERT: L 196 GLU cc_start: 0.6078 (pp20) cc_final: 0.5816 (pp20) outliers start: 23 outliers final: 19 residues processed: 142 average time/residue: 0.0669 time to fit residues: 12.9838 Evaluate side-chains 140 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 156 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 71 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.183003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.145350 restraints weight = 11695.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.149621 restraints weight = 6296.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.152412 restraints weight = 4354.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153653 restraints weight = 3475.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.155040 restraints weight = 3085.265| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7664 Z= 0.151 Angle : 0.642 9.203 10454 Z= 0.327 Chirality : 0.043 0.124 1178 Planarity : 0.004 0.038 1292 Dihedral : 4.152 19.598 1039 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.35 % Allowed : 21.04 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.19 (0.28), residues: 958 helix: 0.98 (0.27), residues: 387 sheet: -0.51 (0.38), residues: 194 loop : -1.00 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.027 0.002 TYR A 310 PHE 0.026 0.002 PHE A 466 TRP 0.041 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7659) covalent geometry : angle 0.64116 / 0.33 (10444) SS BOND : bond 0.00283 / 0.18 ( 5) SS BOND : angle 1.06046 / 0.58 ( 10) hydrogen bonds : bond 0.03990 / 2.76 ( 375) hydrogen bonds : angle 4.99981 / 3.55 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.363 Fit side-chains REVERT: A 78 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.6565 (t80) REVERT: A 97 ILE cc_start: 0.8503 (mm) cc_final: 0.8209 (mt) REVERT: A 121 CYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7910 (p) REVERT: A 226 TRP cc_start: 0.7108 (m100) cc_final: 0.6716 (p-90) REVERT: A 299 TRP cc_start: 0.8091 (m100) cc_final: 0.7686 (m100) REVERT: A 517 MET cc_start: 0.7564 (mmm) cc_final: 0.7206 (mmm) REVERT: H 73 ASP cc_start: 0.7899 (t0) cc_final: 0.7689 (t70) REVERT: H 76 ARG cc_start: 0.8644 (mtm180) cc_final: 0.8429 (ptt90) REVERT: H 94 TYR cc_start: 0.8755 (m-80) cc_final: 0.8347 (m-80) REVERT: L 3 VAL cc_start: 0.8959 (t) cc_final: 0.8756 (p) REVERT: L 164 TRP cc_start: 0.7837 (m-90) cc_final: 0.7637 (m-90) REVERT: L 196 GLU cc_start: 0.5966 (pp20) cc_final: 0.5712 (pp20) outliers start: 19 outliers final: 16 residues processed: 141 average time/residue: 0.0735 time to fit residues: 14.4406 Evaluate side-chains 141 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 564 CYS Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain L residue 137 LEU Chi-restraints excluded: chain L residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.0070 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.184140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.147722 restraints weight = 11609.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.151998 restraints weight = 6185.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.154803 restraints weight = 4232.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.156501 restraints weight = 3355.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157403 restraints weight = 2908.773| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7664 Z= 0.131 Angle : 0.633 8.431 10454 Z= 0.322 Chirality : 0.043 0.178 1178 Planarity : 0.004 0.038 1292 Dihedral : 4.060 17.396 1039 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.48 % Allowed : 21.66 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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 are not related in a simple way. whole: -0.11 (0.28), residues: 958 helix: 1.11 (0.27), residues: 385 sheet: -0.49 (0.38), residues: 194 loop : -1.01 (0.34), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.027 0.001 TYR A 310 PHE 0.021 0.001 PHE A 466 TRP 0.035 0.001 TRP L 164 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7659) covalent geometry : angle 0.63265 / 0.32 (10444) SS BOND : bond 0.00250 / 0.15 ( 5) SS BOND : angle 0.90911 / 0.50 ( 10) hydrogen bonds : bond 0.03842 / 2.65 ( 375) hydrogen bonds : angle 4.98182 / 3.53 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.33 seconds wall clock time: 22 minutes 51.00 seconds (1371.00 seconds total)