Starting phenix.real_space_refine on Fri Aug 22 18:37:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjn_17713/08_2025/8pjn_17713.map" } resolution = 3.4 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 7 5.49 5 S 51 5.16 5 C 4382 2.51 5 N 1231 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6917 Number of models: 1 Model: "" Number of chains: 6 Chain: "b" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2134 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 13, 'HIS:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 127 Chain: "2" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1212 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 144} Chain breaks: 1 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 43 Chain: "i" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3017 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 17, 'TRANS': 377} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'GLU:plan': 15, 'ASP:plan': 9, 'GLN:plan1': 3, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 114 Chain: "u" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1865 SG CYS b 354 34.319 76.743 20.414 1.00 38.66 S ATOM 2005 SG CYS b 374 34.034 73.285 21.978 1.00 43.27 S ATOM 2030 SG CYS b 377 32.056 76.493 23.338 1.00 44.14 S ATOM 5669 SG CYS i 302 63.822 66.968 20.941 1.00 25.69 S ATOM 5746 SG CYS i 314 65.272 68.705 24.005 1.00 25.97 S ATOM 5766 SG CYS i 317 66.348 69.591 20.248 1.00 26.45 S Time building chain proxies: 1.77, per 1000 atoms: 0.26 Number of scatterers: 6917 At special positions: 0 Unit cell: (123.395, 110.63, 105.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 51 16.00 P 7 15.00 O 1244 8.00 N 1231 7.00 C 4382 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 339.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN b 501 " pdb="ZN ZN b 501 " - pdb=" ND1 HIS b 356 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 354 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 374 " pdb="ZN ZN b 501 " - pdb=" SG CYS b 377 " pdb=" ZN i 401 " pdb="ZN ZN i 401 " - pdb=" NE2 HIS b 331 " pdb="ZN ZN i 401 " - pdb=" SG CYS i 302 " pdb="ZN ZN i 401 " - pdb=" SG CYS i 317 " pdb="ZN ZN i 401 " - pdb=" SG CYS i 314 " Number of angles added : 6 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1752 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 62.2% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'b' and resid 1 through 46 removed outlier: 3.613A pdb=" N GLU b 10 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE b 43 " --> pdb=" O LEU b 39 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN b 45 " --> pdb=" O HIS b 41 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER b 46 " --> pdb=" O GLU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 81 removed outlier: 4.273A pdb=" N LEU b 59 " --> pdb=" O GLY b 55 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL b 60 " --> pdb=" O THR b 56 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS b 79 " --> pdb=" O LEU b 75 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 97 removed outlier: 4.091A pdb=" N VAL b 86 " --> pdb=" O ILE b 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER b 87 " --> pdb=" O HIS b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 112 through 129 removed outlier: 4.487A pdb=" N ARG b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU b 117 " --> pdb=" O ASP b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 143 removed outlier: 3.506A pdb=" N GLU b 141 " --> pdb=" O GLU b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 165 Proline residue: b 153 - end of helix removed outlier: 3.726A pdb=" N GLU b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU b 157 " --> pdb=" O PRO b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 262 through 275 Processing helix chain 'b' and resid 280 through 306 Proline residue: b 294 - end of helix removed outlier: 5.124A pdb=" N ASN b 298 " --> pdb=" O PRO b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 325 through 329 removed outlier: 3.734A pdb=" N TRP b 329 " --> pdb=" O LYS b 326 " (cutoff:3.500A) Processing helix chain 'b' and resid 360 through 366 Processing helix chain '2' and resid 8 through 21 Processing helix chain '2' and resid 88 through 93 Processing helix chain '2' and resid 100 through 108 Processing helix chain '2' and resid 108 through 115 Processing helix chain '2' and resid 123 through 133 removed outlier: 3.679A pdb=" N HIS 2 132 " --> pdb=" O ALA 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 133 through 148 Processing helix chain 'i' and resid 6 through 18 Processing helix chain 'i' and resid 19 through 60 Proline residue: i 25 - end of helix removed outlier: 3.660A pdb=" N VAL i 50 " --> pdb=" O HIS i 46 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER i 59 " --> pdb=" O GLU i 55 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY i 60 " --> pdb=" O LYS i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 108 removed outlier: 4.260A pdb=" N SER i 69 " --> pdb=" O ASP i 65 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU i 70 " --> pdb=" O SER i 66 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 111 No H-bonds generated for 'chain 'i' and resid 109 through 111' Processing helix chain 'i' and resid 116 through 137 Processing helix chain 'i' and resid 138 through 150 removed outlier: 3.588A pdb=" N ALA i 142 " --> pdb=" O TYR i 138 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 172 Processing helix chain 'i' and resid 176 through 185 Processing helix chain 'i' and resid 185 through 192 Processing helix chain 'i' and resid 195 through 211 removed outlier: 3.711A pdb=" N SER i 199 " --> pdb=" O CYS i 195 " (cutoff:3.500A) Processing helix chain 'i' and resid 213 through 225 Processing helix chain 'i' and resid 226 through 229 removed outlier: 7.472A pdb=" N GLU i 229 " --> pdb=" O SER i 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 226 through 229' Processing helix chain 'i' and resid 230 through 241 Processing helix chain 'i' and resid 242 through 245 Processing helix chain 'i' and resid 251 through 259 removed outlier: 4.928A pdb=" N LEU i 257 " --> pdb=" O PRO i 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP i 259 " --> pdb=" O LYS i 255 " (cutoff:3.500A) Processing helix chain 'i' and resid 261 through 278 removed outlier: 3.517A pdb=" N MET i 265 " --> pdb=" O ALA i 261 " (cutoff:3.500A) Processing helix chain 'i' and resid 284 through 298 Processing helix chain 'i' and resid 299 through 304 removed outlier: 3.970A pdb=" N LYS i 304 " --> pdb=" O GLN i 301 " (cutoff:3.500A) Processing helix chain 'i' and resid 314 through 317 Processing helix chain 'i' and resid 318 through 325 Processing helix chain 'i' and resid 364 through 371 Processing helix chain 'i' and resid 386 through 390 Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'u' and resid 37 through 39 No H-bonds generated for 'chain 'u' and resid 37 through 39' Processing helix chain 'u' and resid 55 through 60 removed outlier: 3.650A pdb=" N TYR u 59 " --> pdb=" O THR u 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 357 through 359 Processing sheet with id=AA2, first strand: chain 'b' and resid 372 through 373 Processing sheet with id=AA3, first strand: chain '2' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'i' and resid 361 through 363 Processing sheet with id=AA5, first strand: chain 'i' and resid 376 through 377 Processing sheet with id=AA6, first strand: chain 'u' and resid 12 through 16 removed outlier: 4.064A pdb=" N SER u 65 " --> pdb=" O GLN u 2 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1203 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: 0.67 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1253 1.33 - 1.45: 1623 1.45 - 1.57: 4086 1.57 - 1.69: 7 1.69 - 1.81: 75 Bond restraints: 7044 Sorted by residual: bond pdb=" O2P SEP 2 171 " pdb=" P SEP 2 171 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O2P SEP 2 168 " pdb=" P SEP 2 168 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O1P SEP 2 168 " pdb=" P SEP 2 168 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P SEP 2 168 " pdb=" P SEP 2 168 " ideal model delta sigma weight residual 1.610 1.512 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O1P SEP 2 169 " pdb=" P SEP 2 169 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 7039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 9148 1.73 - 3.47: 339 3.47 - 5.20: 68 5.20 - 6.93: 3 6.93 - 8.67: 8 Bond angle restraints: 9566 Sorted by residual: angle pdb=" N CYS i 178 " pdb=" CA CYS i 178 " pdb=" C CYS i 178 " ideal model delta sigma weight residual 111.28 106.48 4.80 1.09e+00 8.42e-01 1.94e+01 angle pdb=" C TYR b 35 " pdb=" N THR b 36 " pdb=" CA THR b 36 " ideal model delta sigma weight residual 120.28 114.56 5.72 1.44e+00 4.82e-01 1.58e+01 angle pdb=" N ASN b 368 " pdb=" CA ASN b 368 " pdb=" C ASN b 368 " ideal model delta sigma weight residual 112.72 108.52 4.20 1.14e+00 7.69e-01 1.36e+01 angle pdb=" CA GLU b 31 " pdb=" C GLU b 31 " pdb=" O GLU b 31 " ideal model delta sigma weight residual 121.00 117.41 3.59 1.05e+00 9.07e-01 1.17e+01 angle pdb=" N ILE 2 145 " pdb=" CA ILE 2 145 " pdb=" C ILE 2 145 " ideal model delta sigma weight residual 110.72 107.32 3.40 1.01e+00 9.80e-01 1.13e+01 ... (remaining 9561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 3872 17.47 - 34.93: 338 34.93 - 52.40: 60 52.40 - 69.86: 18 69.86 - 87.33: 5 Dihedral angle restraints: 4293 sinusoidal: 1598 harmonic: 2695 Sorted by residual: dihedral pdb=" CA PRO b 294 " pdb=" C PRO b 294 " pdb=" N ALA b 295 " pdb=" CA ALA b 295 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASP i 216 " pdb=" CB ASP i 216 " pdb=" CG ASP i 216 " pdb=" OD1 ASP i 216 " ideal model delta sinusoidal sigma weight residual -30.00 -89.97 59.97 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA GLN i 17 " pdb=" C GLN i 17 " pdb=" N GLU i 18 " pdb=" CA GLU i 18 " ideal model delta harmonic sigma weight residual -180.00 -163.08 -16.92 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 4290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 782 0.039 - 0.078: 218 0.078 - 0.117: 90 0.117 - 0.156: 17 0.156 - 0.195: 7 Chirality restraints: 1114 Sorted by residual: chirality pdb=" CA PHE b 367 " pdb=" N PHE b 367 " pdb=" C PHE b 367 " pdb=" CB PHE b 367 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA ILE 2 145 " pdb=" N ILE 2 145 " pdb=" C ILE 2 145 " pdb=" CB ILE 2 145 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA MET b 366 " pdb=" N MET b 366 " pdb=" C MET b 366 " pdb=" CB MET b 366 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 1111 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 340 " 0.248 9.50e-02 1.11e+02 1.11e-01 7.61e+00 pdb=" NE ARG b 340 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG b 340 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG b 340 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG b 340 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR b 71 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C THR b 71 " -0.037 2.00e-02 2.50e+03 pdb=" O THR b 71 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL b 72 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS b 69 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LYS b 69 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS b 69 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP b 70 " 0.011 2.00e-02 2.50e+03 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1339 2.78 - 3.31: 6503 3.31 - 3.84: 10731 3.84 - 4.37: 11829 4.37 - 4.90: 21585 Nonbonded interactions: 51987 Sorted by model distance: nonbonded pdb=" OG SER i 194 " pdb=" OD2 ASP i 273 " model vdw 2.251 3.040 nonbonded pdb=" OD2 ASP i 126 " pdb=" OG SER i 149 " model vdw 2.255 3.040 nonbonded pdb=" O2P SEP 2 171 " pdb=" OG SER i 187 " model vdw 2.363 3.040 nonbonded pdb=" O PHE b 334 " pdb=" OG SER i 336 " model vdw 2.373 3.040 nonbonded pdb=" OE2 GLU i 167 " pdb=" NH1 ARG i 271 " model vdw 2.393 3.120 ... (remaining 51982 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: 1.970 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.140 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.007 0.102 7053 Z= 0.395 Angle : 0.748 8.666 9572 Z= 0.434 Chirality : 0.045 0.195 1114 Planarity : 0.006 0.111 1216 Dihedral : 14.181 87.330 2541 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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 aren not related in a simple way. whole: 1.04 (0.29), residues: 901 helix: 2.01 (0.24), residues: 494 sheet: 0.82 (0.74), residues: 51 loop : -1.31 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG i 210 TYR 0.011 0.001 TYR 2 130 PHE 0.012 0.001 PHE 2 63 TRP 0.011 0.001 TRP i 181 HIS 0.007 0.001 HIS i 183 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 7044) covalent geometry : angle 0.73444 ( 9566) hydrogen bonds : bond 0.14965 ( 413) hydrogen bonds : angle 4.92542 ( 1203) metal coordination : bond 0.02261 ( 8) metal coordination : angle 5.68416 ( 6) Misc. bond : bond 0.08212 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.175 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0668 time to fit residues: 10.3334 Evaluate side-chains 94 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0570 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.105755 restraints weight = 9587.489| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.59 r_work: 0.2942 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7053 Z= 0.123 Angle : 0.501 6.132 9572 Z= 0.254 Chirality : 0.039 0.157 1114 Planarity : 0.004 0.049 1216 Dihedral : 4.127 31.877 1010 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.59 % Allowed : 5.80 % Favored : 92.61 % 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 aren not related in a simple way. whole: 1.47 (0.29), residues: 901 helix: 2.46 (0.23), residues: 505 sheet: 0.55 (0.72), residues: 59 loop : -1.38 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 210 TYR 0.009 0.001 TYR i 275 PHE 0.012 0.001 PHE 2 63 TRP 0.007 0.001 TRP i 120 HIS 0.004 0.001 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7044) covalent geometry : angle 0.50038 ( 9566) hydrogen bonds : bond 0.04835 ( 413) hydrogen bonds : angle 3.75128 ( 1203) metal coordination : bond 0.00464 ( 8) metal coordination : angle 1.33587 ( 6) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.177 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 106 average time/residue: 0.0670 time to fit residues: 9.6889 Evaluate side-chains 105 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 209 ILE Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.122624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.100606 restraints weight = 9662.880| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.73 r_work: 0.2916 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7053 Z= 0.120 Angle : 0.483 6.559 9572 Z= 0.243 Chirality : 0.039 0.156 1114 Planarity : 0.004 0.056 1216 Dihedral : 4.062 29.836 1010 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.74 % Allowed : 9.86 % Favored : 88.41 % 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 aren not related in a simple way. whole: 1.68 (0.30), residues: 901 helix: 2.66 (0.23), residues: 505 sheet: 0.51 (0.71), residues: 59 loop : -1.29 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 173 TYR 0.010 0.001 TYR i 275 PHE 0.010 0.001 PHE 2 63 TRP 0.007 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7044) covalent geometry : angle 0.48147 ( 9566) hydrogen bonds : bond 0.04629 ( 413) hydrogen bonds : angle 3.68301 ( 1203) metal coordination : bond 0.00444 ( 8) metal coordination : angle 1.46973 ( 6) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.216 Fit side-chains REVERT: 2 60 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7882 (mttm) REVERT: i 153 ASP cc_start: 0.8945 (t0) cc_final: 0.8493 (t0) outliers start: 12 outliers final: 11 residues processed: 112 average time/residue: 0.0562 time to fit residues: 9.0166 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.121203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.100038 restraints weight = 9763.365| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.76 r_work: 0.2897 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7053 Z= 0.130 Angle : 0.486 6.785 9572 Z= 0.246 Chirality : 0.039 0.155 1114 Planarity : 0.004 0.058 1216 Dihedral : 4.113 31.386 1010 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.32 % Allowed : 11.30 % Favored : 86.38 % 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 aren not related in a simple way. whole: 1.74 (0.30), residues: 901 helix: 2.72 (0.23), residues: 505 sheet: 0.46 (0.70), residues: 59 loop : -1.28 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.010 0.001 TYR i 275 PHE 0.010 0.001 PHE 2 63 TRP 0.006 0.001 TRP i 181 HIS 0.004 0.001 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 7044) covalent geometry : angle 0.48481 ( 9566) hydrogen bonds : bond 0.04716 ( 413) hydrogen bonds : angle 3.67317 ( 1203) metal coordination : bond 0.00457 ( 8) metal coordination : angle 1.43107 ( 6) Misc. bond : bond 0.00026 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.270 Fit side-chains REVERT: i 153 ASP cc_start: 0.8955 (t0) cc_final: 0.8446 (t0) REVERT: i 240 MET cc_start: 0.8826 (mmt) cc_final: 0.8243 (mmt) outliers start: 16 outliers final: 13 residues processed: 110 average time/residue: 0.0628 time to fit residues: 10.0029 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.102098 restraints weight = 9702.136| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.72 r_work: 0.2934 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7053 Z= 0.105 Angle : 0.463 6.377 9572 Z= 0.234 Chirality : 0.038 0.147 1114 Planarity : 0.004 0.059 1216 Dihedral : 4.016 31.824 1010 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.46 % Allowed : 12.61 % Favored : 84.93 % 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 aren not related in a simple way. whole: 1.81 (0.30), residues: 901 helix: 2.78 (0.23), residues: 505 sheet: 0.50 (0.71), residues: 59 loop : -1.25 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.009 0.001 TYR i 275 PHE 0.012 0.001 PHE i 225 TRP 0.008 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 7044) covalent geometry : angle 0.46210 ( 9566) hydrogen bonds : bond 0.04202 ( 413) hydrogen bonds : angle 3.56702 ( 1203) metal coordination : bond 0.00353 ( 8) metal coordination : angle 1.23165 ( 6) Misc. bond : bond 0.00040 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.208 Fit side-chains REVERT: 2 60 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7820 (mttm) REVERT: i 153 ASP cc_start: 0.8922 (t0) cc_final: 0.8401 (t0) REVERT: u 70 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8219 (m) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.0583 time to fit residues: 9.5205 Evaluate side-chains 119 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 4 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.122497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100848 restraints weight = 9756.900| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.67 r_work: 0.2901 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7053 Z= 0.134 Angle : 0.490 5.843 9572 Z= 0.249 Chirality : 0.039 0.154 1114 Planarity : 0.004 0.058 1216 Dihedral : 4.141 34.961 1010 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.61 % Allowed : 13.19 % Favored : 84.20 % 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 aren not related in a simple way. whole: 1.74 (0.30), residues: 901 helix: 2.71 (0.23), residues: 507 sheet: 0.40 (0.69), residues: 59 loop : -1.29 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.010 0.001 TYR i 275 PHE 0.011 0.001 PHE i 385 TRP 0.006 0.001 TRP i 181 HIS 0.004 0.001 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 7044) covalent geometry : angle 0.48898 ( 9566) hydrogen bonds : bond 0.04741 ( 413) hydrogen bonds : angle 3.64583 ( 1203) metal coordination : bond 0.00462 ( 8) metal coordination : angle 1.38704 ( 6) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.287 Fit side-chains REVERT: b 31 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8261 (tm-30) REVERT: 2 60 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7899 (mttm) REVERT: i 153 ASP cc_start: 0.8959 (t0) cc_final: 0.8399 (t0) REVERT: i 240 MET cc_start: 0.8826 (mmt) cc_final: 0.8467 (mmt) REVERT: u 70 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8269 (m) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.0628 time to fit residues: 10.1094 Evaluate side-chains 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 46 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.121032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.098746 restraints weight = 9754.224| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.71 r_work: 0.2910 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7053 Z= 0.112 Angle : 0.469 7.381 9572 Z= 0.238 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.057 1216 Dihedral : 4.086 35.634 1010 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.19 % Allowed : 13.33 % Favored : 83.48 % 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 aren not related in a simple way. whole: 1.84 (0.30), residues: 901 helix: 2.80 (0.23), residues: 505 sheet: 0.56 (0.71), residues: 53 loop : -1.22 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.009 0.001 TYR i 275 PHE 0.012 0.001 PHE i 225 TRP 0.007 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7044) covalent geometry : angle 0.46866 ( 9566) hydrogen bonds : bond 0.04335 ( 413) hydrogen bonds : angle 3.56317 ( 1203) metal coordination : bond 0.00365 ( 8) metal coordination : angle 1.17146 ( 6) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.222 Fit side-chains REVERT: 2 60 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7862 (mttm) REVERT: i 153 ASP cc_start: 0.8976 (t0) cc_final: 0.8378 (t0) REVERT: i 240 MET cc_start: 0.8767 (mmt) cc_final: 0.8414 (mmt) REVERT: u 70 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8252 (m) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.0640 time to fit residues: 10.5588 Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.098398 restraints weight = 9901.035| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.73 r_work: 0.2905 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7053 Z= 0.119 Angle : 0.488 6.978 9572 Z= 0.248 Chirality : 0.039 0.150 1114 Planarity : 0.004 0.057 1216 Dihedral : 4.095 36.835 1010 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 13.62 % Favored : 83.33 % 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 aren not related in a simple way. whole: 1.86 (0.30), residues: 901 helix: 2.79 (0.23), residues: 507 sheet: 0.68 (0.73), residues: 53 loop : -1.20 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.009 0.001 TYR i 275 PHE 0.014 0.001 PHE i 225 TRP 0.006 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7044) covalent geometry : angle 0.48680 ( 9566) hydrogen bonds : bond 0.04400 ( 413) hydrogen bonds : angle 3.55433 ( 1203) metal coordination : bond 0.00465 ( 8) metal coordination : angle 1.37607 ( 6) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.276 Fit side-chains REVERT: b 31 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8276 (tm-30) REVERT: 2 60 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7882 (mttm) REVERT: i 153 ASP cc_start: 0.8972 (t0) cc_final: 0.8355 (t0) REVERT: i 240 MET cc_start: 0.8766 (mmt) cc_final: 0.8136 (mmt) REVERT: u 70 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8222 (m) outliers start: 21 outliers final: 17 residues processed: 110 average time/residue: 0.0578 time to fit residues: 9.3167 Evaluate side-chains 120 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 357 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 56 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 29 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.101650 restraints weight = 9698.498| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.64 r_work: 0.2947 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7053 Z= 0.102 Angle : 0.475 7.050 9572 Z= 0.242 Chirality : 0.038 0.145 1114 Planarity : 0.004 0.055 1216 Dihedral : 4.009 36.435 1010 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.90 % Allowed : 13.62 % Favored : 83.48 % 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 aren not related in a simple way. whole: 1.96 (0.30), residues: 901 helix: 2.89 (0.23), residues: 506 sheet: 0.75 (0.73), residues: 53 loop : -1.19 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG i 173 TYR 0.009 0.001 TYR b 35 PHE 0.015 0.001 PHE i 225 TRP 0.009 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7044) covalent geometry : angle 0.47351 ( 9566) hydrogen bonds : bond 0.03952 ( 413) hydrogen bonds : angle 3.43849 ( 1203) metal coordination : bond 0.00386 ( 8) metal coordination : angle 1.31428 ( 6) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.265 Fit side-chains REVERT: b 31 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8298 (tm-30) REVERT: b 73 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: i 153 ASP cc_start: 0.8933 (t0) cc_final: 0.8328 (t0) REVERT: i 240 MET cc_start: 0.8803 (mmt) cc_final: 0.8142 (mmt) REVERT: u 70 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8178 (m) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.0629 time to fit residues: 10.2255 Evaluate side-chains 121 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 73 GLN Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 305 GLN Chi-restraints excluded: chain b residue 357 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 0.0060 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.0050 overall best weight: 0.4410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.101772 restraints weight = 9669.653| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.64 r_work: 0.2951 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7053 Z= 0.100 Angle : 0.469 6.965 9572 Z= 0.240 Chirality : 0.038 0.145 1114 Planarity : 0.004 0.054 1216 Dihedral : 3.966 36.101 1010 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.61 % Allowed : 14.20 % Favored : 83.19 % 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 aren not related in a simple way. whole: 2.04 (0.30), residues: 901 helix: 2.92 (0.23), residues: 509 sheet: 0.80 (0.74), residues: 53 loop : -1.14 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 173 TYR 0.008 0.001 TYR b 35 PHE 0.011 0.001 PHE i 225 TRP 0.009 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7044) covalent geometry : angle 0.46837 ( 9566) hydrogen bonds : bond 0.03825 ( 413) hydrogen bonds : angle 3.35287 ( 1203) metal coordination : bond 0.00420 ( 8) metal coordination : angle 1.21556 ( 6) Misc. bond : bond 0.00041 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1802 Ramachandran restraints generated. 901 Oldfield, 0 Emsley, 901 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 0.236 Fit side-chains REVERT: b 31 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8252 (tm-30) REVERT: i 153 ASP cc_start: 0.8918 (t0) cc_final: 0.8329 (t0) REVERT: i 240 MET cc_start: 0.8670 (mmt) cc_final: 0.8333 (mmt) REVERT: u 70 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8154 (m) outliers start: 18 outliers final: 14 residues processed: 112 average time/residue: 0.0598 time to fit residues: 9.6540 Evaluate side-chains 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 305 GLN Chi-restraints excluded: chain b residue 357 ILE Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 77 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.0070 chunk 88 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 40 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.122963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.101158 restraints weight = 9645.082| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.67 r_work: 0.2965 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7053 Z= 0.100 Angle : 0.471 6.962 9572 Z= 0.240 Chirality : 0.038 0.145 1114 Planarity : 0.004 0.052 1216 Dihedral : 3.940 35.913 1010 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.46 % Allowed : 13.91 % Favored : 83.62 % 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 aren not related in a simple way. whole: 2.04 (0.30), residues: 901 helix: 2.95 (0.23), residues: 509 sheet: 0.71 (0.76), residues: 47 loop : -1.13 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG i 173 TYR 0.011 0.001 TYR b 35 PHE 0.011 0.001 PHE i 225 TRP 0.009 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 7044) covalent geometry : angle 0.46987 ( 9566) hydrogen bonds : bond 0.03738 ( 413) hydrogen bonds : angle 3.34357 ( 1203) metal coordination : bond 0.00413 ( 8) metal coordination : angle 1.24188 ( 6) Misc. bond : bond 0.00042 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1704.54 seconds wall clock time: 29 minutes 47.81 seconds (1787.81 seconds total)