Starting phenix.real_space_refine on Fri Dec 27 22:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_17713.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_17713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_17713.map" model { file = "/net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_17713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pjn_17713/12_2024/8pjn_17713.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 6, '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: {'GLN:plan1': 3, 'GLU:plan': 15, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 9} 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, 'ASN:plan1': 1, 'ASP:plan': 3} 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: 4.79, per 1000 atoms: 0.69 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.70 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: 1.87 Time building geometry restraints manager: 2.14 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: 1.360 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.610 ------------------------------------------------------------------------------- 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 7044 Z= 0.447 Angle : 0.734 8.666 9566 Z= 0.432 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP i 181 HIS 0.007 0.001 HIS i 183 PHE 0.012 0.001 PHE 2 63 TYR 0.011 0.001 TYR 2 130 ARG 0.002 0.000 ARG i 210 *********************** 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 : 0.915 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1775 time to fit residues: 27.0018 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 : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 0.3980 chunk 68 optimal weight: 0.0050 chunk 37 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7044 Z= 0.146 Angle : 0.483 6.172 9566 Z= 0.244 Chirality : 0.038 0.152 1114 Planarity : 0.004 0.049 1216 Dihedral : 4.037 31.258 1010 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.16 % Allowed : 5.94 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.29), residues: 901 helix: 2.51 (0.23), residues: 505 sheet: 0.65 (0.72), residues: 59 loop : -1.35 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.009 0.001 PHE 2 63 TYR 0.009 0.001 TYR 2 61 ARG 0.003 0.000 ARG i 210 *********************** 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: 8 poor density : 105 time to evaluate : 0.793 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 108 average time/residue: 0.1652 time to fit residues: 24.7896 Evaluate side-chains 104 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 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 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7044 Z= 0.184 Angle : 0.483 6.487 9566 Z= 0.243 Chirality : 0.039 0.156 1114 Planarity : 0.004 0.056 1216 Dihedral : 4.018 29.566 1010 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.74 % Allowed : 9.42 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.30), residues: 901 helix: 2.69 (0.23), residues: 505 sheet: 0.59 (0.72), residues: 59 loop : -1.28 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP i 181 HIS 0.003 0.001 HIS i 105 PHE 0.011 0.001 PHE 2 63 TYR 0.010 0.001 TYR i 275 ARG 0.005 0.000 ARG i 173 *********************** 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 118 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.750 Fit side-chains REVERT: i 153 ASP cc_start: 0.8811 (t0) cc_final: 0.8328 (t0) outliers start: 12 outliers final: 11 residues processed: 109 average time/residue: 0.1618 time to fit residues: 24.9320 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.0010 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 73 GLN b 346 ASN i 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7044 Z= 0.151 Angle : 0.457 6.115 9566 Z= 0.231 Chirality : 0.038 0.151 1114 Planarity : 0.004 0.058 1216 Dihedral : 3.948 29.550 1010 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 11.01 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.30), residues: 901 helix: 2.84 (0.23), residues: 505 sheet: 0.59 (0.72), residues: 59 loop : -1.22 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 PHE 0.009 0.001 PHE i 385 TYR 0.008 0.001 TYR i 275 ARG 0.007 0.000 ARG i 173 *********************** 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 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.835 Fit side-chains REVERT: i 153 ASP cc_start: 0.8798 (t0) cc_final: 0.8271 (t0) REVERT: i 240 MET cc_start: 0.8623 (mmt) cc_final: 0.7974 (mmt) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.1587 time to fit residues: 24.3742 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 78 optimal weight: 0.0270 chunk 21 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 GLN b 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7044 Z= 0.138 Angle : 0.450 7.066 9566 Z= 0.227 Chirality : 0.038 0.149 1114 Planarity : 0.004 0.059 1216 Dihedral : 3.874 28.760 1010 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.32 % Allowed : 12.03 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.30), residues: 901 helix: 2.88 (0.23), residues: 508 sheet: 0.65 (0.71), residues: 59 loop : -1.20 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 PHE 0.014 0.001 PHE i 225 TYR 0.007 0.001 TYR i 275 ARG 0.007 0.000 ARG i 173 *********************** 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: 16 poor density : 106 time to evaluate : 0.850 Fit side-chains REVERT: i 41 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: i 153 ASP cc_start: 0.8767 (t0) cc_final: 0.8235 (t0) REVERT: i 240 MET cc_start: 0.8595 (mmt) cc_final: 0.7969 (mmt) outliers start: 16 outliers final: 12 residues processed: 111 average time/residue: 0.1588 time to fit residues: 25.0180 Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 41 ASP 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 Chi-restraints excluded: chain u residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.0070 chunk 40 optimal weight: 0.0000 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 346 ASN i 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7044 Z= 0.129 Angle : 0.440 6.559 9566 Z= 0.222 Chirality : 0.037 0.145 1114 Planarity : 0.004 0.059 1216 Dihedral : 3.767 28.250 1010 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.03 % Allowed : 12.75 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.30), residues: 901 helix: 2.96 (0.23), residues: 509 sheet: 0.96 (0.75), residues: 53 loop : -1.12 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 120 HIS 0.002 0.000 HIS i 105 PHE 0.010 0.001 PHE i 385 TYR 0.007 0.001 TYR i 275 ARG 0.007 0.000 ARG i 173 *********************** 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 122 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.834 Fit side-chains REVERT: i 41 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: i 153 ASP cc_start: 0.8704 (t0) cc_final: 0.8202 (t0) REVERT: i 240 MET cc_start: 0.8491 (mmt) cc_final: 0.8111 (mmt) REVERT: u 70 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8295 (m) outliers start: 14 outliers final: 9 residues processed: 113 average time/residue: 0.1556 time to fit residues: 24.9839 Evaluate side-chains 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 2 residue 79 ILE Chi-restraints excluded: chain i residue 41 ASP Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 313 ASP 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 63 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.1980 chunk 48 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7044 Z= 0.144 Angle : 0.452 6.368 9566 Z= 0.229 Chirality : 0.038 0.148 1114 Planarity : 0.004 0.056 1216 Dihedral : 3.779 28.372 1010 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.32 % Allowed : 13.33 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.30), residues: 901 helix: 2.99 (0.23), residues: 509 sheet: 0.91 (0.74), residues: 53 loop : -1.11 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 PHE 0.013 0.001 PHE i 225 TYR 0.010 0.001 TYR b 35 ARG 0.008 0.000 ARG i 173 *********************** 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 119 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.807 Fit side-chains REVERT: i 153 ASP cc_start: 0.8714 (t0) cc_final: 0.8183 (t0) REVERT: i 240 MET cc_start: 0.8522 (mmt) cc_final: 0.7956 (mmt) REVERT: u 70 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8308 (m) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.1529 time to fit residues: 24.6345 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 68 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7044 Z= 0.181 Angle : 0.487 7.585 9566 Z= 0.247 Chirality : 0.039 0.153 1114 Planarity : 0.004 0.053 1216 Dihedral : 3.934 30.802 1010 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.03 % Allowed : 14.06 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 901 helix: 2.93 (0.23), residues: 509 sheet: 0.85 (0.73), residues: 53 loop : -1.11 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 181 HIS 0.003 0.001 HIS i 105 PHE 0.015 0.001 PHE i 225 TYR 0.013 0.001 TYR b 35 ARG 0.007 0.000 ARG i 173 *********************** 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 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.853 Fit side-chains REVERT: i 153 ASP cc_start: 0.8809 (t0) cc_final: 0.8201 (t0) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.1674 time to fit residues: 25.7144 Evaluate side-chains 113 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7044 Z= 0.166 Angle : 0.479 7.344 9566 Z= 0.244 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.054 1216 Dihedral : 3.934 31.421 1010 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.17 % Allowed : 13.77 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.30), residues: 901 helix: 2.96 (0.23), residues: 507 sheet: 0.71 (0.73), residues: 59 loop : -1.17 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 PHE 0.016 0.001 PHE i 225 TYR 0.009 0.001 TYR b 35 ARG 0.008 0.000 ARG i 173 *********************** 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 116 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.760 Fit side-chains REVERT: i 153 ASP cc_start: 0.8804 (t0) cc_final: 0.8189 (t0) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 0.1604 time to fit residues: 24.2044 Evaluate side-chains 112 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 0.0040 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7044 Z= 0.165 Angle : 0.477 7.294 9566 Z= 0.243 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.051 1216 Dihedral : 3.936 32.388 1010 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 14.06 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.30), residues: 901 helix: 2.96 (0.23), residues: 507 sheet: 0.69 (0.73), residues: 59 loop : -1.17 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.018 0.001 PHE i 225 TYR 0.008 0.001 TYR b 35 ARG 0.007 0.000 ARG i 173 ********************** 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 117 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.822 Fit side-chains REVERT: i 153 ASP cc_start: 0.8814 (t0) cc_final: 0.8182 (t0) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 0.1572 time to fit residues: 24.2634 Evaluate side-chains 114 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.123717 restraints weight = 9707.488| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.90 r_work: 0.3275 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7044 Z= 0.168 Angle : 0.478 7.236 9566 Z= 0.244 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.050 1216 Dihedral : 3.963 33.396 1010 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.88 % Allowed : 14.20 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.30), residues: 901 helix: 2.95 (0.23), residues: 509 sheet: 0.65 (0.72), residues: 59 loop : -1.15 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.011 0.001 PHE i 225 TYR 0.009 0.001 TYR b 35 ARG 0.007 0.000 ARG i 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1665.51 seconds wall clock time: 31 minutes 0.87 seconds (1860.87 seconds total)