Starting phenix.real_space_refine on Sat Apr 6 03:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/04_2024/8pjn_17713_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.33, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 37 helices and 4 sheets defined 55.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'b' and resid 2 through 45 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) Processing helix chain 'b' and resid 55 through 96 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) removed outlier: 3.993A pdb=" N ILE b 82 " --> pdb=" O ASP b 78 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS b 83 " --> pdb=" O HIS b 79 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER b 84 " --> pdb=" O LYS b 80 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) 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 113 through 128 removed outlier: 4.259A pdb=" N LEU b 117 " --> pdb=" O ASP b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 142 removed outlier: 3.506A pdb=" N GLU b 141 " --> pdb=" O GLU b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 148 through 164 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 263 through 274 Processing helix chain 'b' and resid 281 through 305 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 326 through 328 No H-bonds generated for 'chain 'b' and resid 326 through 328' Processing helix chain 'b' and resid 360 through 366 Processing helix chain '2' and resid 8 through 20 Processing helix chain '2' and resid 89 through 92 No H-bonds generated for 'chain '2' and resid 89 through 92' Processing helix chain '2' and resid 101 through 107 Processing helix chain '2' and resid 109 through 114 Processing helix chain '2' and resid 124 through 132 removed outlier: 3.679A pdb=" N HIS 2 132 " --> pdb=" O ALA 2 128 " (cutoff:3.500A) Processing helix chain '2' and resid 134 through 147 Processing helix chain 'i' and resid 7 through 17 Processing helix chain 'i' and resid 20 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 110 removed outlier: 4.369A pdb=" N VAL i 68 " --> pdb=" O ASP i 65 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER i 69 " --> pdb=" O SER i 66 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU i 87 " --> pdb=" O LYS i 84 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS i 109 " --> pdb=" O LEU i 106 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER i 110 " --> pdb=" O LYS i 107 " (cutoff:3.500A) Processing helix chain 'i' and resid 117 through 136 Processing helix chain 'i' and resid 139 through 149 Processing helix chain 'i' and resid 158 through 172 Processing helix chain 'i' and resid 177 through 184 Processing helix chain 'i' and resid 186 through 191 Processing helix chain 'i' and resid 196 through 210 Processing helix chain 'i' and resid 214 through 227 removed outlier: 4.236A pdb=" N SER i 226 " --> pdb=" O ARG i 222 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN i 227 " --> pdb=" O LYS i 223 " (cutoff:3.500A) Processing helix chain 'i' and resid 230 through 244 removed outlier: 3.885A pdb=" N ALA i 244 " --> pdb=" O GLY i 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 252 through 258 removed outlier: 4.928A pdb=" N LEU i 257 " --> pdb=" O PRO i 253 " (cutoff:3.500A) Processing helix chain 'i' and resid 262 through 277 Processing helix chain 'i' and resid 285 through 297 Processing helix chain 'i' and resid 300 through 303 Processing helix chain 'i' and resid 315 through 317 No H-bonds generated for 'chain 'i' and resid 315 through 317' Processing helix chain 'i' and resid 319 through 324 Processing helix chain 'i' and resid 364 through 370 Processing helix chain 'i' and resid 387 through 389 No H-bonds generated for 'chain 'i' and resid 387 through 389' Processing helix chain 'u' and resid 23 through 33 Processing helix chain 'u' and resid 38 through 40 No H-bonds generated for 'chain 'u' and resid 38 through 40' Processing helix chain 'u' and resid 56 through 59 No H-bonds generated for 'chain 'u' and resid 56 through 59' Processing sheet with id= A, first strand: chain 'b' and resid 349 through 351 Processing sheet with id= B, first strand: chain '2' and resid 25 through 27 Processing sheet with id= C, first strand: chain 'i' and resid 353 through 355 Processing sheet with id= D, first strand: chain 'u' and resid 12 through 16 removed outlier: 6.040A pdb=" N SER u 65 " --> pdb=" O PHE u 4 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LYS u 6 " --> pdb=" O SER u 65 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU u 67 " --> pdb=" O LYS u 6 " (cutoff:3.500A) 352 hydrogen bonds defined for protein. 900 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: 1.76 Time building geometry restraints manager: 2.90 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: 100.01 - 106.88: 236 106.88 - 113.74: 4014 113.74 - 120.60: 2932 120.60 - 127.46: 2319 127.46 - 134.32: 65 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: 1.51 - 2.19: 1 2.19 - 2.87: 2445 2.87 - 3.54: 9549 3.54 - 4.22: 14103 4.22 - 4.90: 26137 Nonbonded interactions: 52235 Sorted by model distance: nonbonded pdb=" NZ LYS 2 87 " pdb=" C GLY u 76 " model vdw 1.512 3.350 nonbonded pdb=" OG SER i 194 " pdb=" OD2 ASP i 273 " model vdw 2.251 2.440 nonbonded pdb=" OD2 ASP i 126 " pdb=" OG SER i 149 " model vdw 2.255 2.440 nonbonded pdb=" O2P SEP 2 171 " pdb=" OG SER i 187 " model vdw 2.363 2.440 nonbonded pdb=" O PHE b 334 " pdb=" OG SER i 336 " model vdw 2.373 2.440 ... (remaining 52230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.050 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: 4.380 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.190 Find NCS groups from input model: 0.180 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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= 0.466 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 : 1.512 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 fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.847 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1795 time to fit residues: 27.3387 Evaluate side-chains 94 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 0.9990 chunk 68 optimal weight: 0.0570 chunk 37 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.0470 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 346 ASN i 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0722 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= 0.145 Angle : 0.474 6.384 9566 Z= 0.245 Chirality : 0.038 0.153 1114 Planarity : 0.004 0.040 1216 Dihedral : 3.885 28.686 1010 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.45 % Allowed : 4.78 % Favored : 93.77 % 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: 1.13 (0.29), residues: 901 helix: 2.01 (0.23), residues: 502 sheet: 0.86 (0.75), residues: 53 loop : -1.22 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.010 0.001 PHE 2 63 TYR 0.010 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 108 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.823 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.1639 time to fit residues: 23.4365 Evaluate side-chains 103 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 136 CYS 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 45 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 0.0970 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 346 ASN i 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0959 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= 0.164 Angle : 0.462 6.372 9566 Z= 0.236 Chirality : 0.038 0.156 1114 Planarity : 0.004 0.043 1216 Dihedral : 3.903 30.417 1010 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.74 % Allowed : 10.14 % Favored : 88.12 % 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: 1.24 (0.29), residues: 901 helix: 2.10 (0.24), residues: 499 sheet: 0.82 (0.74), residues: 53 loop : -1.14 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.009 0.001 PHE 2 63 TYR 0.008 0.001 TYR b 21 ARG 0.006 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 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 0.764 Fit side-chains REVERT: i 240 MET cc_start: 0.8581 (mmt) cc_final: 0.8203 (mmt) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.1802 time to fit residues: 26.8780 Evaluate side-chains 108 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 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 61 optimal weight: 5.9990 chunk 42 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1126 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= 0.186 Angle : 0.469 6.568 9566 Z= 0.239 Chirality : 0.038 0.157 1114 Planarity : 0.004 0.047 1216 Dihedral : 3.990 32.346 1010 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.03 % Allowed : 12.17 % Favored : 85.80 % 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: 1.23 (0.29), residues: 901 helix: 2.10 (0.24), residues: 500 sheet: 0.72 (0.72), residues: 53 loop : -1.15 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.010 0.001 PHE 2 63 TYR 0.008 0.001 TYR b 21 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 115 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.816 Fit side-chains REVERT: i 153 ASP cc_start: 0.8895 (t0) cc_final: 0.8350 (t0) outliers start: 14 outliers final: 12 residues processed: 106 average time/residue: 0.1570 time to fit residues: 23.6054 Evaluate side-chains 108 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 chunk 21 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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: 0.8360 moved from start: 0.1196 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= 0.162 Angle : 0.454 6.918 9566 Z= 0.232 Chirality : 0.038 0.151 1114 Planarity : 0.004 0.045 1216 Dihedral : 3.946 32.372 1010 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.46 % Allowed : 12.46 % Favored : 85.07 % 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: 1.27 (0.29), residues: 901 helix: 2.14 (0.24), residues: 498 sheet: 0.80 (0.73), residues: 53 loop : -1.15 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.008 0.001 PHE 2 63 TYR 0.007 0.001 TYR i 275 ARG 0.005 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 115 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.683 Fit side-chains REVERT: i 153 ASP cc_start: 0.8913 (t0) cc_final: 0.8313 (t0) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.1633 time to fit residues: 24.3927 Evaluate side-chains 111 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 131 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** i 268 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7044 Z= 0.191 Angle : 0.468 7.210 9566 Z= 0.239 Chirality : 0.038 0.153 1114 Planarity : 0.004 0.044 1216 Dihedral : 4.031 33.185 1010 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.17 % Allowed : 13.62 % 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 (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: 1.24 (0.29), residues: 901 helix: 2.13 (0.24), residues: 499 sheet: 0.82 (0.74), residues: 53 loop : -1.19 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.009 0.001 PHE i 225 TYR 0.008 0.001 TYR i 275 ARG 0.003 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 113 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.815 Fit side-chains REVERT: b 31 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8172 (tm-30) REVERT: i 153 ASP cc_start: 0.8906 (t0) cc_final: 0.8278 (t0) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.1595 time to fit residues: 23.3265 Evaluate side-chains 110 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 131 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 40 optimal weight: 0.0030 chunk 53 optimal weight: 0.5980 chunk 34 optimal weight: 0.0670 chunk 51 optimal weight: 0.9990 overall best weight: 0.4128 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1368 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= 0.134 Angle : 0.439 7.374 9566 Z= 0.223 Chirality : 0.037 0.146 1114 Planarity : 0.004 0.045 1216 Dihedral : 3.860 32.186 1010 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.03 % Allowed : 13.91 % 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: 1.32 (0.29), residues: 901 helix: 2.17 (0.24), residues: 501 sheet: 1.00 (0.74), residues: 53 loop : -1.16 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.008 0.001 PHE i 225 TYR 0.006 0.001 TYR b 35 ARG 0.003 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 117 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.746 Fit side-chains REVERT: b 317 GLU cc_start: 0.8448 (tt0) cc_final: 0.8228 (tt0) REVERT: i 153 ASP cc_start: 0.8871 (t0) cc_final: 0.8244 (t0) outliers start: 14 outliers final: 11 residues processed: 111 average time/residue: 0.1538 time to fit residues: 24.3199 Evaluate side-chains 109 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 131 MET 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 2 residue 79 ILE Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 156 ASN Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR 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: 5.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8402 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7044 Z= 0.231 Angle : 0.500 7.286 9566 Z= 0.257 Chirality : 0.039 0.155 1114 Planarity : 0.004 0.044 1216 Dihedral : 4.096 35.961 1010 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % 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: 1.21 (0.29), residues: 901 helix: 2.10 (0.24), residues: 500 sheet: 0.78 (0.74), residues: 53 loop : -1.19 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP b 312 HIS 0.002 0.000 HIS i 220 PHE 0.010 0.001 PHE 2 63 TYR 0.009 0.001 TYR i 275 ARG 0.003 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 109 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.826 Fit side-chains REVERT: i 153 ASP cc_start: 0.8919 (t0) cc_final: 0.8234 (t0) outliers start: 14 outliers final: 12 residues processed: 101 average time/residue: 0.1470 time to fit residues: 21.2729 Evaluate side-chains 106 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 131 MET Chi-restraints excluded: chain b residue 132 LEU 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 156 ASN Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 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 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1459 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= 0.144 Angle : 0.461 7.692 9566 Z= 0.237 Chirality : 0.038 0.155 1114 Planarity : 0.004 0.045 1216 Dihedral : 3.915 35.261 1010 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.88 % Allowed : 14.49 % 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 (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: 1.33 (0.29), residues: 901 helix: 2.18 (0.24), residues: 499 sheet: 0.88 (0.74), residues: 53 loop : -1.10 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.009 0.001 PHE i 225 TYR 0.007 0.001 TYR b 35 ARG 0.003 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 111 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.781 Fit side-chains REVERT: b 317 GLU cc_start: 0.8455 (tt0) cc_final: 0.8240 (tt0) REVERT: i 153 ASP cc_start: 0.8900 (t0) cc_final: 0.8231 (t0) outliers start: 13 outliers final: 12 residues processed: 104 average time/residue: 0.1571 time to fit residues: 23.3197 Evaluate side-chains 108 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 131 MET Chi-restraints excluded: chain b residue 132 LEU 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 2 residue 79 ILE Chi-restraints excluded: chain i residue 156 ASN Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 0.1980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 0.0570 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7044 Z= 0.138 Angle : 0.460 7.740 9566 Z= 0.236 Chirality : 0.038 0.146 1114 Planarity : 0.004 0.044 1216 Dihedral : 3.819 34.396 1010 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.88 % Allowed : 15.22 % Favored : 82.90 % 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: 1.40 (0.29), residues: 901 helix: 2.25 (0.24), residues: 499 sheet: 0.93 (0.77), residues: 47 loop : -1.08 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.009 0.001 PHE i 225 TYR 0.009 0.001 TYR b 35 ARG 0.003 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 107 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.837 Fit side-chains REVERT: i 153 ASP cc_start: 0.8880 (t0) cc_final: 0.8216 (t0) outliers start: 13 outliers final: 10 residues processed: 100 average time/residue: 0.1556 time to fit residues: 22.2601 Evaluate side-chains 104 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 132 LEU 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 2 residue 79 ILE Chi-restraints excluded: chain i residue 156 ASN 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: 2.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121598 restraints weight = 9587.343| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.88 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7044 Z= 0.176 Angle : 0.476 7.515 9566 Z= 0.244 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.044 1216 Dihedral : 3.908 36.004 1010 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.03 % Allowed : 15.65 % Favored : 82.32 % 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: 1.40 (0.29), residues: 901 helix: 2.25 (0.24), residues: 500 sheet: 0.89 (0.77), residues: 47 loop : -1.08 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP i 120 HIS 0.002 0.000 HIS i 220 PHE 0.009 0.001 PHE i 225 TYR 0.013 0.001 TYR b 35 ARG 0.003 0.000 ARG i 173 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.65 seconds wall clock time: 31 minutes 58.73 seconds (1918.73 seconds total)