Starting phenix.real_space_refine on Tue Aug 4 18:55:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190.map" model { file = "/net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q3e_72190/08_2026/9q3e_72190_neut.cif" } resolution = 3.3 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= 0.001 sd= 0.019 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 Zn 3 6.06 5 S 49 5.16 5 C 3866 2.51 5 N 1025 2.21 5 O 1085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6028 Number of models: 1 Model: "" Number of chains: 5 Chain: "N" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3454 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 12, 'TRANS': 435} Chain breaks: 2 Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 364 Unresolved non-hydrogen dihedrals: 254 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 5, 'ASN:plan1': 7, 'ASP:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 15, 'HIS:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 198 Chain: "B" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 669 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "C" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 752 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 6, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 30 Chain: "L" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1150 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 141} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 309 SG CYS N 42 30.692 73.541 28.670 1.00 50.62 S ATOM 331 SG CYS N 45 28.195 71.976 25.780 1.00 87.16 S ATOM 472 SG CYS N 63 30.254 75.355 25.706 1.00 67.14 S ATOM 497 SG CYS N 66 27.516 74.807 28.201 1.00 86.95 S ATOM 401 SG CYS N 54 28.919 78.685 36.541 1.00 53.46 S ATOM 422 SG CYS N 57 32.213 78.431 38.755 1.00 60.66 S ATOM 545 SG CYS N 72 29.281 76.106 39.405 1.00 59.73 S ATOM 2381 SG CYS N 321 61.813 113.497 44.426 1.00 85.04 S ATOM 2406 SG CYS N 324 61.553 110.263 46.160 1.00103.34 S ATOM 2690 SG CYS N 362 64.940 111.743 45.882 1.00127.30 S Time building chain proxies: 1.26, per 1000 atoms: 0.21 Number of scatterers: 6028 At special positions: 0 Unit cell: (91.388, 124.553, 86.966, 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) Zn 3 29.99 S 49 16.00 O 1085 8.00 N 1025 7.00 C 3866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.48 Conformation dependent library (CDL) restraints added in 231.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 66 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 63 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 42 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 45 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" NE2 HIS N 61 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 72 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 57 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 54 " pdb=" ZN N1003 " pdb="ZN ZN N1003 " - pdb=" NE2 HIS N 311 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 324 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 321 " pdb="ZN ZN N1003 " - pdb=" SG CYS N 362 " Number of angles added : 12 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1522 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 55.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'N' and resid 2 through 12 Processing helix chain 'N' and resid 15 through 22 Processing helix chain 'N' and resid 79 through 84 Processing helix chain 'N' and resid 91 through 106 Processing helix chain 'N' and resid 109 through 116 Processing helix chain 'N' and resid 135 through 139 Processing helix chain 'N' and resid 182 through 195 removed outlier: 3.647A pdb=" N LEU N 186 " --> pdb=" O ASP N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 198 through 214 removed outlier: 4.264A pdb=" N GLU N 204 " --> pdb=" O SER N 200 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 228 Processing helix chain 'N' and resid 229 through 235 Processing helix chain 'N' and resid 255 through 264 removed outlier: 4.317A pdb=" N CYS N 260 " --> pdb=" O ASN N 257 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU N 262 " --> pdb=" O ALA N 259 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL N 263 " --> pdb=" O CYS N 260 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS N 264 " --> pdb=" O LYS N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 274 Processing helix chain 'N' and resid 287 through 300 Processing helix chain 'N' and resid 301 through 302 No H-bonds generated for 'chain 'N' and resid 301 through 302' Processing helix chain 'N' and resid 303 through 309 Processing helix chain 'N' and resid 314 through 318 removed outlier: 3.805A pdb=" N VAL N 318 " --> pdb=" O ALA N 315 " (cutoff:3.500A) Processing helix chain 'N' and resid 330 through 334 removed outlier: 3.853A pdb=" N TRP N 333 " --> pdb=" O TYR N 330 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN N 334 " --> pdb=" O THR N 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 330 through 334' Processing helix chain 'N' and resid 335 through 357 removed outlier: 3.662A pdb=" N LYS N 339 " --> pdb=" O ASP N 335 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.743A pdb=" N VAL N 372 " --> pdb=" O ILE N 368 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU N 373 " --> pdb=" O TYR N 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 368 through 373' Processing helix chain 'N' and resid 380 through 395 Processing helix chain 'N' and resid 413 through 424 Processing helix chain 'N' and resid 433 through 446 Processing helix chain 'N' and resid 457 through 461 Processing helix chain 'N' and resid 462 through 470 removed outlier: 3.702A pdb=" N ARG N 468 " --> pdb=" O ASP N 464 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N HIS N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 36 removed outlier: 3.502A pdb=" N LEU B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'C' and resid 52 through 58 Processing helix chain 'C' and resid 66 through 84 removed outlier: 4.084A pdb=" N LYS C 72 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 111 removed outlier: 3.548A pdb=" N LEU C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 46 Processing helix chain 'L' and resid 53 through 67 Processing helix chain 'L' and resid 69 through 88 Processing helix chain 'L' and resid 88 through 95 Processing helix chain 'L' and resid 100 through 123 removed outlier: 3.650A pdb=" N THR L 104 " --> pdb=" O ASN L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 135 removed outlier: 4.268A pdb=" N VAL L 131 " --> pdb=" O ASP L 127 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 151 Processing helix chain 'L' and resid 154 through 168 Processing sheet with id=AA1, first strand: chain 'N' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain 'N' and resid 52 through 53 removed outlier: 3.505A pdb=" N VAL N 62 " --> pdb=" O THR N 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'N' and resid 242 through 249 Processing sheet with id=AA5, first strand: chain 'N' and resid 405 through 407 Processing sheet with id=AA6, first strand: chain 'B' and resid 49 through 50 removed outlier: 9.403A pdb=" N ALA B 73 " --> pdb=" O ASP B 2 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE B 4 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL B 75 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET B 6 " --> pdb=" O VAL B 75 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N LEU B 77 " --> pdb=" O MET B 6 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG B 8 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N PHE B 79 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS C 32 " --> pdb=" O PHE B 15 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N ASP B 17 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL C 60 " --> pdb=" O TYR C 18 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS C 20 " --> pdb=" O VAL C 60 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 876 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: 0.93 Time building geometry restraints manager: 0.65 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: 1932 1.34 - 1.46: 1462 1.46 - 1.58: 2683 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 6149 Sorted by residual: bond pdb=" N PRO N 78 " pdb=" CA PRO N 78 " ideal model delta sigma weight residual 1.469 1.449 0.020 7.40e-03 1.83e+04 7.00e+00 bond pdb=" CB CYS N 46 " pdb=" SG CYS N 46 " ideal model delta sigma weight residual 1.808 1.745 0.063 3.30e-02 9.18e+02 3.68e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N HIS B 10 " pdb=" CA HIS B 10 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.84e+00 bond pdb=" C ARG B 9 " pdb=" N HIS B 10 " ideal model delta sigma weight residual 1.332 1.309 0.023 1.40e-02 5.10e+03 2.80e+00 ... (remaining 6144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8060 1.94 - 3.87: 242 3.87 - 5.81: 55 5.81 - 7.74: 5 7.74 - 9.68: 2 Bond angle restraints: 8364 Sorted by residual: angle pdb=" N VAL N 189 " pdb=" CA VAL N 189 " pdb=" C VAL N 189 " ideal model delta sigma weight residual 111.44 104.15 7.29 1.34e+00 5.57e-01 2.96e+01 angle pdb=" CA ASP N 187 " pdb=" CB ASP N 187 " pdb=" CG ASP N 187 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N ASP N 187 " pdb=" CA ASP N 187 " pdb=" C ASP N 187 " ideal model delta sigma weight residual 111.71 107.54 4.17 1.15e+00 7.56e-01 1.31e+01 angle pdb=" CA ASP N 188 " pdb=" CB ASP N 188 " pdb=" CG ASP N 188 " ideal model delta sigma weight residual 112.60 115.78 -3.18 1.00e+00 1.00e+00 1.01e+01 angle pdb=" C ASP B 47 " pdb=" CA ASP B 47 " pdb=" CB ASP B 47 " ideal model delta sigma weight residual 117.23 113.08 4.15 1.36e+00 5.41e-01 9.32e+00 ... (remaining 8359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.85: 3255 13.85 - 27.70: 270 27.70 - 41.56: 95 41.56 - 55.41: 28 55.41 - 69.26: 11 Dihedral angle restraints: 3659 sinusoidal: 1326 harmonic: 2333 Sorted by residual: dihedral pdb=" CA TYR B 45 " pdb=" C TYR B 45 " pdb=" N LYS B 46 " pdb=" CA LYS B 46 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER N 145 " pdb=" C SER N 145 " pdb=" N MET N 146 " pdb=" CA MET N 146 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA LEU L 85 " pdb=" C LEU L 85 " pdb=" N ILE L 86 " pdb=" CA ILE L 86 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 3656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 822 0.059 - 0.118: 140 0.118 - 0.177: 20 0.177 - 0.236: 1 0.236 - 0.295: 1 Chirality restraints: 984 Sorted by residual: chirality pdb=" CA VAL N 189 " pdb=" N VAL N 189 " pdb=" C VAL N 189 " pdb=" CB VAL N 189 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL N 189 " pdb=" CA VAL N 189 " pdb=" CG1 VAL N 189 " pdb=" CG2 VAL N 189 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 981 not shown) Planarity restraints: 1055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 83 " -0.008 2.00e-02 2.50e+03 1.96e-02 7.68e+00 pdb=" CG TYR C 83 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR C 83 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR C 83 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR C 83 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 83 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR C 83 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 83 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA N 7 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ALA N 7 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA N 7 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS N 8 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 456 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO N 457 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO N 457 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 457 " 0.023 5.00e-02 4.00e+02 ... (remaining 1052 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1297 2.78 - 3.31: 5775 3.31 - 3.84: 9901 3.84 - 4.37: 11881 4.37 - 4.90: 20281 Nonbonded interactions: 49135 Sorted by model distance: nonbonded pdb=" OE1 GLU L 56 " pdb=" NH2 ARG L 59 " model vdw 2.254 3.120 nonbonded pdb=" O CYS N 42 " pdb=" N CYS N 46 " model vdw 2.289 3.120 nonbonded pdb=" N GLN N 429 " pdb=" OE1 GLN N 429 " model vdw 2.301 3.120 nonbonded pdb=" N GLU C 54 " pdb=" OE1 GLU C 54 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU L 55 " pdb=" NH1 ARG L 59 " model vdw 2.352 3.120 ... (remaining 49130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.890 Find NCS groups from input model: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 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 : 0.005 0.063 6161 Z= 0.231 Angle : 0.874 15.710 8376 Z= 0.449 Chirality : 0.046 0.295 984 Planarity : 0.005 0.053 1055 Dihedral : 13.374 69.258 2137 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.16 % Allowed : 13.94 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 769 helix: 0.31 (0.26), residues: 378 sheet: 0.35 (0.62), residues: 62 loop : -0.59 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 128 TYR 0.041 0.003 TYR C 83 PHE 0.016 0.002 PHE B 79 TRP 0.023 0.003 TRP L 34 HIS 0.007 0.002 HIS N 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 6149) covalent geometry : angle 0.82512 / 0.45 ( 8364) hydrogen bonds : bond 0.13863 / 9.40 ( 313) hydrogen bonds : angle 6.08595 / 4.51 ( 876) metal coordination : bond 0.01807 / 1.50 ( 12) metal coordination : angle 7.63711 / 4.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.230 Fit side-chains REVERT: N 82 ARG cc_start: 0.7888 (tpt90) cc_final: 0.7221 (tpt170) REVERT: N 101 MET cc_start: 0.7930 (ttp) cc_final: 0.7712 (ttt) REVERT: N 183 LYS cc_start: 0.7676 (mttt) cc_final: 0.7472 (mttt) REVERT: N 188 ASP cc_start: 0.7668 (t0) cc_final: 0.7322 (t0) REVERT: N 208 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7631 (mtt180) REVERT: N 209 TYR cc_start: 0.8605 (t80) cc_final: 0.8386 (t80) REVERT: N 347 ASN cc_start: 0.8313 (t0) cc_final: 0.8092 (t0) REVERT: N 388 ILE cc_start: 0.8115 (mt) cc_final: 0.7841 (mp) REVERT: N 433 LEU cc_start: 0.8284 (tp) cc_final: 0.8075 (tp) REVERT: N 436 VAL cc_start: 0.8258 (t) cc_final: 0.8010 (m) REVERT: N 467 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7493 (mtt-85) REVERT: B 4 PHE cc_start: 0.7807 (m-80) cc_final: 0.7448 (m-10) REVERT: L 59 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7338 (ttp-110) REVERT: L 69 HIS cc_start: 0.8053 (m-70) cc_final: 0.7835 (m90) REVERT: L 87 ASN cc_start: 0.8276 (m-40) cc_final: 0.8006 (m110) REVERT: L 134 ASN cc_start: 0.8155 (m-40) cc_final: 0.7811 (m110) REVERT: L 150 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7198 (mm-40) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.0985 time to fit residues: 20.5547 Evaluate side-chains 158 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 59 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 190 ASN C 35 HIS L 60 ASN L 67 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.124766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.112197 restraints weight = 8871.569| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.79 r_work: 0.3370 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6161 Z= 0.156 Angle : 0.550 8.969 8376 Z= 0.286 Chirality : 0.041 0.155 984 Planarity : 0.004 0.053 1055 Dihedral : 4.745 49.836 849 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.04 % Allowed : 12.82 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 769 helix: 0.96 (0.26), residues: 381 sheet: 0.46 (0.61), residues: 64 loop : -0.90 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 128 TYR 0.016 0.002 TYR C 79 PHE 0.019 0.002 PHE B 15 TRP 0.013 0.002 TRP L 34 HIS 0.005 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 6149) covalent geometry : angle 0.51699 / 0.28 ( 8364) hydrogen bonds : bond 0.04542 / 3.16 ( 313) hydrogen bonds : angle 4.79912 / 3.44 ( 876) metal coordination : bond 0.01705 / 1.42 ( 12) metal coordination : angle 4.98528 / 3.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.251 Fit side-chains REVERT: N 4 PHE cc_start: 0.7211 (t80) cc_final: 0.6978 (t80) REVERT: N 82 ARG cc_start: 0.8096 (tpt90) cc_final: 0.7541 (tpt90) REVERT: N 100 ASP cc_start: 0.7517 (m-30) cc_final: 0.7116 (m-30) REVERT: N 101 MET cc_start: 0.8122 (ttp) cc_final: 0.7844 (ttp) REVERT: N 151 ASP cc_start: 0.7368 (t0) cc_final: 0.7070 (m-30) REVERT: N 188 ASP cc_start: 0.7528 (t0) cc_final: 0.7220 (t0) REVERT: N 190 ASN cc_start: 0.8032 (m-40) cc_final: 0.7755 (m110) REVERT: N 262 LEU cc_start: 0.7957 (mt) cc_final: 0.7692 (mp) REVERT: N 388 ILE cc_start: 0.7850 (mt) cc_final: 0.7613 (mp) REVERT: B 8 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8027 (mtp180) REVERT: L 87 ASN cc_start: 0.8241 (m-40) cc_final: 0.8039 (m110) REVERT: L 100 ASN cc_start: 0.7447 (m-40) cc_final: 0.7215 (m110) REVERT: L 134 ASN cc_start: 0.8259 (m-40) cc_final: 0.7938 (m-40) REVERT: L 150 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7506 (mm-40) outliers start: 19 outliers final: 12 residues processed: 180 average time/residue: 0.1011 time to fit residues: 23.0521 Evaluate side-chains 176 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111135 restraints weight = 8848.963| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.79 r_work: 0.3353 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6161 Z= 0.177 Angle : 0.552 9.161 8376 Z= 0.283 Chirality : 0.042 0.154 984 Planarity : 0.004 0.054 1055 Dihedral : 4.301 17.669 845 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.69 % Allowed : 14.10 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.29), residues: 769 helix: 1.04 (0.27), residues: 387 sheet: 0.61 (0.62), residues: 64 loop : -1.05 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 82 TYR 0.018 0.002 TYR C 79 PHE 0.012 0.002 PHE B 93 TRP 0.010 0.002 TRP L 34 HIS 0.006 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.18 ( 6149) covalent geometry : angle 0.51503 / 0.28 ( 8364) hydrogen bonds : bond 0.04559 / 3.17 ( 313) hydrogen bonds : angle 4.66524 / 3.34 ( 876) metal coordination : bond 0.01632 / 1.33 ( 12) metal coordination : angle 5.30382 / 3.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.234 Fit side-chains REVERT: N 101 MET cc_start: 0.8198 (ttp) cc_final: 0.7953 (ttp) REVERT: N 187 ASP cc_start: 0.7957 (m-30) cc_final: 0.7742 (m-30) REVERT: N 188 ASP cc_start: 0.7526 (t0) cc_final: 0.7220 (t0) REVERT: N 211 SER cc_start: 0.8181 (m) cc_final: 0.7978 (t) REVERT: N 262 LEU cc_start: 0.7913 (mt) cc_final: 0.7656 (mp) REVERT: B 4 PHE cc_start: 0.8033 (m-80) cc_final: 0.7807 (m-10) REVERT: B 8 ARG cc_start: 0.8307 (mtp180) cc_final: 0.8024 (mtp180) REVERT: C 63 ARG cc_start: 0.8203 (mmt180) cc_final: 0.8002 (mmt-90) REVERT: L 87 ASN cc_start: 0.8311 (m-40) cc_final: 0.8104 (m110) REVERT: L 100 ASN cc_start: 0.7466 (m110) cc_final: 0.7237 (m110) REVERT: L 134 ASN cc_start: 0.8254 (m-40) cc_final: 0.7924 (m-40) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 0.0952 time to fit residues: 22.3952 Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 301 LEU Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 459 VAL Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 74 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 97 ASN ** N 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 GLN L 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112783 restraints weight = 8939.207| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.73 r_work: 0.3357 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6161 Z= 0.175 Angle : 0.531 7.991 8376 Z= 0.275 Chirality : 0.041 0.149 984 Planarity : 0.004 0.053 1055 Dihedral : 4.248 19.099 845 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.53 % Allowed : 15.22 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.29), residues: 769 helix: 0.87 (0.26), residues: 396 sheet: 0.74 (0.63), residues: 64 loop : -1.22 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 286 TYR 0.017 0.002 TYR C 79 PHE 0.014 0.002 PHE N 4 TRP 0.010 0.001 TRP L 109 HIS 0.005 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6149) covalent geometry : angle 0.50061 / 0.27 ( 8364) hydrogen bonds : bond 0.04387 / 3.05 ( 313) hydrogen bonds : angle 4.59671 / 3.29 ( 876) metal coordination : bond 0.01648 / 1.34 ( 12) metal coordination : angle 4.68965 / 2.98 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.235 Fit side-chains REVERT: N 82 ARG cc_start: 0.8104 (tpt90) cc_final: 0.7690 (tpt90) REVERT: N 101 MET cc_start: 0.8203 (ttp) cc_final: 0.7947 (ttp) REVERT: N 151 ASP cc_start: 0.7140 (m-30) cc_final: 0.6891 (m-30) REVERT: N 187 ASP cc_start: 0.8031 (m-30) cc_final: 0.7755 (m-30) REVERT: N 188 ASP cc_start: 0.7490 (t0) cc_final: 0.7177 (t0) REVERT: N 209 TYR cc_start: 0.8581 (t80) cc_final: 0.8337 (t80) REVERT: N 211 SER cc_start: 0.8193 (m) cc_final: 0.7932 (m) REVERT: N 262 LEU cc_start: 0.7956 (mt) cc_final: 0.7703 (mp) REVERT: B 8 ARG cc_start: 0.8333 (mtp180) cc_final: 0.8029 (mtp180) REVERT: C 63 ARG cc_start: 0.8184 (mmt180) cc_final: 0.7969 (mmt-90) REVERT: C 105 MET cc_start: 0.7807 (mmm) cc_final: 0.7324 (mmt) REVERT: L 64 MET cc_start: 0.8387 (ttm) cc_final: 0.8163 (ttp) REVERT: L 100 ASN cc_start: 0.7488 (m110) cc_final: 0.7281 (m110) REVERT: L 133 GLN cc_start: 0.7939 (mt0) cc_final: 0.7712 (mt0) REVERT: L 134 ASN cc_start: 0.8218 (m-40) cc_final: 0.7857 (m110) REVERT: L 152 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7751 (t) outliers start: 22 outliers final: 16 residues processed: 184 average time/residue: 0.0959 time to fit residues: 22.3959 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 463 ILE Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.0870 chunk 29 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113409 restraints weight = 8927.838| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.73 r_work: 0.3375 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6161 Z= 0.159 Angle : 0.516 7.803 8376 Z= 0.267 Chirality : 0.041 0.159 984 Planarity : 0.004 0.054 1055 Dihedral : 4.168 18.281 845 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.37 % Allowed : 14.58 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 769 helix: 1.05 (0.26), residues: 395 sheet: 0.77 (0.63), residues: 64 loop : -1.23 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 286 TYR 0.014 0.001 TYR N 160 PHE 0.023 0.002 PHE B 4 TRP 0.011 0.001 TRP L 109 HIS 0.004 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 6149) covalent geometry : angle 0.48872 / 0.26 ( 8364) hydrogen bonds : bond 0.04231 / 2.93 ( 313) hydrogen bonds : angle 4.45463 / 3.18 ( 876) metal coordination : bond 0.01518 / 1.22 ( 12) metal coordination : angle 4.37858 / 2.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 0.231 Fit side-chains REVERT: N 65 TRP cc_start: 0.8390 (m100) cc_final: 0.8183 (m100) REVERT: N 101 MET cc_start: 0.8208 (ttp) cc_final: 0.7945 (ttp) REVERT: N 151 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6865 (m-30) REVERT: N 183 LYS cc_start: 0.7864 (mttt) cc_final: 0.7657 (mttt) REVERT: N 188 ASP cc_start: 0.7482 (t0) cc_final: 0.7181 (t0) REVERT: N 211 SER cc_start: 0.8181 (m) cc_final: 0.7962 (t) REVERT: N 262 LEU cc_start: 0.7952 (mt) cc_final: 0.7696 (mp) REVERT: N 465 LYS cc_start: 0.8190 (mptp) cc_final: 0.7842 (mptp) REVERT: B 4 PHE cc_start: 0.8039 (m-80) cc_final: 0.7803 (m-10) REVERT: B 8 ARG cc_start: 0.8337 (mtp180) cc_final: 0.8044 (mtp180) REVERT: C 105 MET cc_start: 0.7799 (mmm) cc_final: 0.7336 (mmt) REVERT: L 64 MET cc_start: 0.8387 (ttm) cc_final: 0.8170 (ttp) REVERT: L 100 ASN cc_start: 0.7495 (m110) cc_final: 0.7288 (m110) REVERT: L 133 GLN cc_start: 0.7929 (mt0) cc_final: 0.7713 (mt0) REVERT: L 134 ASN cc_start: 0.8210 (m-40) cc_final: 0.7859 (m110) REVERT: L 152 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7744 (t) outliers start: 21 outliers final: 15 residues processed: 182 average time/residue: 0.0971 time to fit residues: 22.4320 Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 30 optimal weight: 0.2980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 190 ASN N 441 GLN L 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114866 restraints weight = 8830.663| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.59 r_work: 0.3406 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6161 Z= 0.125 Angle : 0.497 7.045 8376 Z= 0.258 Chirality : 0.040 0.163 984 Planarity : 0.003 0.053 1055 Dihedral : 3.987 17.861 845 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.04 % Allowed : 16.35 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.30), residues: 769 helix: 1.34 (0.27), residues: 386 sheet: 0.86 (0.63), residues: 64 loop : -0.99 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 82 TYR 0.015 0.001 TYR N 209 PHE 0.019 0.001 PHE B 4 TRP 0.010 0.001 TRP L 109 HIS 0.003 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6149) covalent geometry : angle 0.47899 / 0.26 ( 8364) hydrogen bonds : bond 0.03944 / 2.74 ( 313) hydrogen bonds : angle 4.35089 / 3.10 ( 876) metal coordination : bond 0.01270 / 1.05 ( 12) metal coordination : angle 3.49361 / 2.20 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.251 Fit side-chains REVERT: N 82 ARG cc_start: 0.8043 (tpt90) cc_final: 0.7706 (tpt170) REVERT: N 101 MET cc_start: 0.8182 (ttp) cc_final: 0.7883 (ttp) REVERT: N 151 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6836 (m-30) REVERT: N 211 SER cc_start: 0.8120 (m) cc_final: 0.7866 (m) REVERT: N 262 LEU cc_start: 0.7915 (mt) cc_final: 0.7681 (mp) REVERT: N 451 ARG cc_start: 0.7404 (mtm110) cc_final: 0.7106 (mtm180) REVERT: N 465 LYS cc_start: 0.8191 (mptp) cc_final: 0.7854 (mptp) REVERT: B 8 ARG cc_start: 0.8291 (mtp180) cc_final: 0.7992 (mtp180) REVERT: C 37 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8393 (mp) REVERT: C 105 MET cc_start: 0.7784 (mmm) cc_final: 0.7321 (mmt) REVERT: L 100 ASN cc_start: 0.7514 (m110) cc_final: 0.7299 (m110) REVERT: L 134 ASN cc_start: 0.8191 (m-40) cc_final: 0.7852 (m110) outliers start: 19 outliers final: 12 residues processed: 174 average time/residue: 0.0998 time to fit residues: 21.8655 Evaluate side-chains 177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 69 optimal weight: 0.2980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 87 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114034 restraints weight = 8807.047| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.71 r_work: 0.3378 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6161 Z= 0.143 Angle : 0.516 7.455 8376 Z= 0.264 Chirality : 0.040 0.150 984 Planarity : 0.003 0.052 1055 Dihedral : 4.022 18.111 845 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.53 % Allowed : 17.31 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.38 (0.30), residues: 769 helix: 1.21 (0.27), residues: 395 sheet: 0.92 (0.63), residues: 64 loop : -1.16 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 82 TYR 0.021 0.002 TYR N 445 PHE 0.018 0.001 PHE N 280 TRP 0.010 0.001 TRP L 109 HIS 0.003 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6149) covalent geometry : angle 0.49730 / 0.26 ( 8364) hydrogen bonds : bond 0.04042 / 2.81 ( 313) hydrogen bonds : angle 4.37389 / 3.13 ( 876) metal coordination : bond 0.01333 / 1.09 ( 12) metal coordination : angle 3.71206 / 2.33 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 0.236 Fit side-chains REVERT: N 82 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7695 (tpt170) REVERT: N 101 MET cc_start: 0.8207 (ttp) cc_final: 0.7897 (ttp) REVERT: N 151 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: N 187 ASP cc_start: 0.7991 (m-30) cc_final: 0.7536 (m-30) REVERT: N 211 SER cc_start: 0.8115 (m) cc_final: 0.7869 (m) REVERT: N 262 LEU cc_start: 0.7904 (mt) cc_final: 0.7668 (mp) REVERT: N 465 LYS cc_start: 0.8191 (mptp) cc_final: 0.7907 (mptp) REVERT: B 8 ARG cc_start: 0.8332 (mtp180) cc_final: 0.8049 (mtp180) REVERT: C 37 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8364 (mp) REVERT: C 105 MET cc_start: 0.7828 (mmm) cc_final: 0.7377 (mmt) REVERT: L 100 ASN cc_start: 0.7555 (m110) cc_final: 0.7351 (m110) REVERT: L 134 ASN cc_start: 0.8208 (m-40) cc_final: 0.7880 (m-40) outliers start: 22 outliers final: 14 residues processed: 180 average time/residue: 0.0947 time to fit residues: 21.7161 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 272 MET Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 57 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.125596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.113692 restraints weight = 8816.444| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.72 r_work: 0.3377 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6161 Z= 0.163 Angle : 0.537 7.660 8376 Z= 0.274 Chirality : 0.041 0.155 984 Planarity : 0.003 0.053 1055 Dihedral : 4.113 18.611 845 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.53 % Allowed : 17.31 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.30), residues: 769 helix: 1.16 (0.27), residues: 395 sheet: 0.93 (0.63), residues: 64 loop : -1.16 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 82 TYR 0.021 0.002 TYR N 445 PHE 0.018 0.001 PHE N 280 TRP 0.010 0.001 TRP L 109 HIS 0.004 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6149) covalent geometry : angle 0.51598 / 0.27 ( 8364) hydrogen bonds : bond 0.04224 / 2.93 ( 313) hydrogen bonds : angle 4.42958 / 3.17 ( 876) metal coordination : bond 0.01425 / 1.16 ( 12) metal coordination : angle 3.99578 / 2.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.234 Fit side-chains REVERT: N 82 ARG cc_start: 0.8096 (tpt90) cc_final: 0.7699 (tpt170) REVERT: N 101 MET cc_start: 0.8200 (ttp) cc_final: 0.7914 (ttp) REVERT: N 151 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6872 (m-30) REVERT: N 187 ASP cc_start: 0.8011 (m-30) cc_final: 0.7597 (m-30) REVERT: N 188 ASP cc_start: 0.7439 (t0) cc_final: 0.7142 (t0) REVERT: N 211 SER cc_start: 0.8132 (m) cc_final: 0.7882 (m) REVERT: N 262 LEU cc_start: 0.7916 (mt) cc_final: 0.7686 (mp) REVERT: N 465 LYS cc_start: 0.8209 (mptp) cc_final: 0.7915 (mptp) REVERT: B 8 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8062 (mtp180) REVERT: C 37 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8354 (mp) REVERT: C 105 MET cc_start: 0.7825 (mmm) cc_final: 0.7388 (mmt) REVERT: L 100 ASN cc_start: 0.7560 (m110) cc_final: 0.7357 (m110) REVERT: L 134 ASN cc_start: 0.8221 (m-40) cc_final: 0.7915 (m-40) outliers start: 22 outliers final: 16 residues processed: 179 average time/residue: 0.1052 time to fit residues: 23.9297 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 272 MET Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 75 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 169 GLN ** N 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112812 restraints weight = 8850.871| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.72 r_work: 0.3352 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6161 Z= 0.197 Angle : 0.566 8.645 8376 Z= 0.289 Chirality : 0.042 0.159 984 Planarity : 0.004 0.053 1055 Dihedral : 4.292 19.322 845 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.21 % Allowed : 17.79 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 769 helix: 1.04 (0.26), residues: 394 sheet: 1.02 (0.66), residues: 54 loop : -1.18 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 467 TYR 0.022 0.002 TYR N 445 PHE 0.018 0.002 PHE N 280 TRP 0.011 0.002 TRP N 41 HIS 0.008 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.20 ( 6149) covalent geometry : angle 0.53948 / 0.29 ( 8364) hydrogen bonds : bond 0.04483 / 3.11 ( 313) hydrogen bonds : angle 4.50997 / 3.23 ( 876) metal coordination : bond 0.01562 / 1.26 ( 12) metal coordination : angle 4.58177 / 2.90 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.227 Fit side-chains REVERT: N 101 MET cc_start: 0.8196 (ttp) cc_final: 0.7920 (ttp) REVERT: N 151 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: N 188 ASP cc_start: 0.7510 (t0) cc_final: 0.7186 (t0) REVERT: N 211 SER cc_start: 0.8188 (m) cc_final: 0.7968 (t) REVERT: N 262 LEU cc_start: 0.7935 (mt) cc_final: 0.7676 (mp) REVERT: N 451 ARG cc_start: 0.7642 (mtm110) cc_final: 0.7394 (mtm180) REVERT: N 465 LYS cc_start: 0.8230 (mptp) cc_final: 0.7934 (mptp) REVERT: B 8 ARG cc_start: 0.8346 (mtp180) cc_final: 0.8066 (mtp180) REVERT: C 37 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 105 MET cc_start: 0.7853 (mmm) cc_final: 0.7390 (mmt) REVERT: L 134 ASN cc_start: 0.8214 (m-40) cc_final: 0.7924 (m110) outliers start: 20 outliers final: 17 residues processed: 172 average time/residue: 0.0868 time to fit residues: 19.3329 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 272 MET Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 334 ASN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 20 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 63 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 190 ASN N 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114560 restraints weight = 8782.204| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.73 r_work: 0.3376 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6161 Z= 0.136 Angle : 0.669 31.644 8376 Z= 0.280 Chirality : 0.040 0.157 984 Planarity : 0.003 0.053 1055 Dihedral : 4.095 18.010 845 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.30), residues: 769 helix: 1.22 (0.27), residues: 394 sheet: 1.03 (0.66), residues: 54 loop : -1.10 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 467 TYR 0.016 0.002 TYR N 445 PHE 0.018 0.001 PHE N 280 TRP 0.011 0.001 TRP N 65 HIS 0.007 0.001 HIS L 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 6149) covalent geometry : angle 0.50987 / 0.27 ( 8364) hydrogen bonds : bond 0.03974 / 2.77 ( 313) hydrogen bonds : angle 4.38277 / 3.15 ( 876) metal coordination : bond 0.01304 / 1.09 ( 12) metal coordination : angle 11.45410 / 6.43 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.255 Fit side-chains REVERT: N 101 MET cc_start: 0.8204 (ttp) cc_final: 0.7891 (ttp) REVERT: N 151 ASP cc_start: 0.7177 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: N 188 ASP cc_start: 0.7420 (t0) cc_final: 0.7122 (t0) REVERT: N 211 SER cc_start: 0.8155 (m) cc_final: 0.7930 (t) REVERT: N 262 LEU cc_start: 0.7896 (mt) cc_final: 0.7646 (mp) REVERT: N 451 ARG cc_start: 0.7611 (mtm110) cc_final: 0.7150 (mtm180) REVERT: N 465 LYS cc_start: 0.8195 (mptp) cc_final: 0.7824 (mptp) REVERT: B 8 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8096 (mtp180) REVERT: C 37 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8344 (mp) REVERT: C 105 MET cc_start: 0.7828 (mmm) cc_final: 0.7409 (mmt) REVERT: L 133 GLN cc_start: 0.7916 (mt0) cc_final: 0.7678 (mt0) REVERT: L 134 ASN cc_start: 0.8183 (m-40) cc_final: 0.7842 (m110) outliers start: 20 outliers final: 15 residues processed: 169 average time/residue: 0.0944 time to fit residues: 20.5799 Evaluate side-chains 174 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain N residue 151 ASP Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 278 ILE Chi-restraints excluded: chain N residue 291 THR Chi-restraints excluded: chain N residue 292 GLN Chi-restraints excluded: chain N residue 385 LYS Chi-restraints excluded: chain N residue 423 SER Chi-restraints excluded: chain N residue 461 PHE Chi-restraints excluded: chain N residue 462 THR Chi-restraints excluded: chain N residue 466 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.124652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.112871 restraints weight = 8787.126| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.70 r_work: 0.3357 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6161 Z= 0.217 Angle : 0.707 30.468 8376 Z= 0.310 Chirality : 0.043 0.168 984 Planarity : 0.004 0.053 1055 Dihedral : 4.397 21.697 845 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.21 % Allowed : 19.71 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.12 (0.29), residues: 769 helix: 0.97 (0.26), residues: 394 sheet: 1.06 (0.66), residues: 54 loop : -1.22 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 467 TYR 0.045 0.002 TYR N 161 PHE 0.019 0.002 PHE N 280 TRP 0.009 0.002 TRP N 41 HIS 0.005 0.001 HIS N 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.22 ( 6149) covalent geometry : angle 0.56455 / 0.30 ( 8364) hydrogen bonds : bond 0.04602 / 3.21 ( 313) hydrogen bonds : angle 4.55450 / 3.26 ( 876) metal coordination : bond 0.01614 / 1.34 ( 12) metal coordination : angle 11.25639 / 6.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.61 seconds wall clock time: 31 minutes 59.35 seconds (1919.35 seconds total)