Starting phenix.real_space_refine on Fri Jul 19 07:18:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/07_2024/8pjn_17713_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/07_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_17713/07_2024/8pjn_17713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/07_2024/8pjn_17713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/07_2024/8pjn_17713_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pjn_17713/07_2024/8pjn_17713_neut.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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.78, 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 - 3.50 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: 2.88 Conformation dependent library (CDL) restraints added in 1.5 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: 0.89 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: 1.86 Time building geometry restraints manager: 3.17 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: 2437 2.87 - 3.54: 9491 3.54 - 4.22: 13971 4.22 - 4.90: 26091 Nonbonded interactions: 51991 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 51986 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 25.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- 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= 0.441 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 : 0.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1846 time to fit residues: 27.9916 Evaluate side-chains 94 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 0.0020 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.0819 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= 0.179 Angle : 0.493 6.213 9566 Z= 0.250 Chirality : 0.039 0.157 1114 Planarity : 0.004 0.050 1216 Dihedral : 4.036 29.268 1010 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.59 % Allowed : 5.80 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.29), residues: 901 helix: 2.50 (0.23), residues: 504 sheet: 0.73 (0.74), residues: 53 loop : -1.38 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 181 HIS 0.003 0.001 HIS i 105 PHE 0.011 0.001 PHE 2 63 TYR 0.009 0.001 TYR i 275 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 115 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.808 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.1723 time to fit residues: 25.9120 Evaluate side-chains 106 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS 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: 1.9990 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8348 moved from start: 0.1064 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= 0.179 Angle : 0.475 6.634 9566 Z= 0.239 Chirality : 0.038 0.155 1114 Planarity : 0.004 0.059 1216 Dihedral : 4.028 30.912 1010 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.88 % Allowed : 9.86 % Favored : 88.26 % 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: 2.70 (0.23), residues: 505 sheet: 0.71 (0.73), residues: 53 loop : -1.29 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.010 0.001 PHE 2 63 TYR 0.009 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 121 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 0.808 Fit side-chains REVERT: i 153 ASP cc_start: 0.8783 (t0) cc_final: 0.8300 (t0) outliers start: 13 outliers final: 12 residues processed: 112 average time/residue: 0.1565 time to fit residues: 24.8239 Evaluate side-chains 113 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 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: 2.9990 chunk 9 optimal weight: 0.0050 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 73 GLN i 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1163 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= 0.161 Angle : 0.461 6.989 9566 Z= 0.232 Chirality : 0.038 0.151 1114 Planarity : 0.004 0.060 1216 Dihedral : 3.994 31.597 1010 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.17 % Allowed : 11.59 % Favored : 86.23 % 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: 1.81 (0.30), residues: 901 helix: 2.78 (0.23), residues: 505 sheet: 0.72 (0.72), residues: 53 loop : -1.29 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.010 0.001 PHE i 225 TYR 0.009 0.001 TYR i 275 ARG 0.006 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 123 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.797 Fit side-chains REVERT: i 153 ASP cc_start: 0.8783 (t0) cc_final: 0.8243 (t0) REVERT: i 240 MET cc_start: 0.8631 (mmt) cc_final: 0.8248 (mmt) outliers start: 15 outliers final: 12 residues processed: 115 average time/residue: 0.1555 time to fit residues: 25.3464 Evaluate side-chains 116 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 GLN i 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1241 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= 0.187 Angle : 0.473 7.175 9566 Z= 0.239 Chirality : 0.039 0.153 1114 Planarity : 0.004 0.061 1216 Dihedral : 4.045 32.397 1010 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.46 % Allowed : 12.75 % Favored : 84.78 % 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: 1.78 (0.30), residues: 901 helix: 2.78 (0.23), residues: 505 sheet: 0.67 (0.72), residues: 53 loop : -1.32 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 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 120 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 103 time to evaluate : 0.813 Fit side-chains REVERT: b 31 GLU cc_start: 0.8363 (tm-30) cc_final: 0.8161 (tm-30) REVERT: b 73 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: i 153 ASP cc_start: 0.8787 (t0) cc_final: 0.8206 (t0) outliers start: 17 outliers final: 15 residues processed: 109 average time/residue: 0.1544 time to fit residues: 23.9577 Evaluate side-chains 118 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 73 GLN Chi-restraints excluded: chain b residue 78 ASP Chi-restraints excluded: chain b residue 274 LEU Chi-restraints excluded: chain b residue 358 ILE Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 2 residue 68 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 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: 1.9990 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7044 Z= 0.177 Angle : 0.465 6.716 9566 Z= 0.236 Chirality : 0.038 0.150 1114 Planarity : 0.004 0.061 1216 Dihedral : 4.049 32.912 1010 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.61 % Allowed : 13.33 % 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: 1.81 (0.30), residues: 901 helix: 2.81 (0.23), residues: 505 sheet: 0.67 (0.72), residues: 53 loop : -1.31 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP i 120 HIS 0.003 0.001 HIS i 105 PHE 0.014 0.001 PHE i 225 TYR 0.009 0.001 TYR i 275 ARG 0.006 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 fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 0.848 Fit side-chains REVERT: i 153 ASP cc_start: 0.8809 (t0) cc_final: 0.8187 (t0) REVERT: i 240 MET cc_start: 0.8590 (mmt) cc_final: 0.8188 (mmt) outliers start: 18 outliers final: 14 residues processed: 111 average time/residue: 0.1643 time to fit residues: 25.7896 Evaluate side-chains 118 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 156 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.0170 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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: 0.8312 moved from start: 0.1393 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= 0.138 Angle : 0.451 7.646 9566 Z= 0.227 Chirality : 0.038 0.150 1114 Planarity : 0.003 0.060 1216 Dihedral : 3.901 32.123 1010 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.61 % Allowed : 13.33 % 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: 1.95 (0.30), residues: 901 helix: 2.90 (0.23), residues: 507 sheet: 0.86 (0.73), residues: 53 loop : -1.25 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP i 120 HIS 0.003 0.000 HIS i 105 PHE 0.013 0.001 PHE i 225 TYR 0.006 0.001 TYR i 275 ARG 0.007 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 128 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.798 Fit side-chains REVERT: b 317 GLU cc_start: 0.8455 (tt0) cc_final: 0.8240 (tt0) REVERT: i 153 ASP cc_start: 0.8762 (t0) cc_final: 0.8137 (t0) REVERT: i 240 MET cc_start: 0.8617 (mmt) cc_final: 0.8199 (mmt) outliers start: 18 outliers final: 14 residues processed: 116 average time/residue: 0.1616 time to fit residues: 26.1894 Evaluate side-chains 121 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 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 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 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1411 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= 0.166 Angle : 0.466 7.139 9566 Z= 0.236 Chirality : 0.038 0.149 1114 Planarity : 0.004 0.060 1216 Dihedral : 3.924 32.790 1010 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.90 % Allowed : 13.91 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.95 (0.30), residues: 901 helix: 2.87 (0.23), residues: 509 sheet: 0.83 (0.73), residues: 53 loop : -1.23 (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 0.015 0.001 PHE i 225 TYR 0.009 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 128 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 0.809 Fit side-chains REVERT: b 317 GLU cc_start: 0.8457 (tt0) cc_final: 0.8250 (tt0) REVERT: i 153 ASP cc_start: 0.8808 (t0) cc_final: 0.8152 (t0) REVERT: i 240 MET cc_start: 0.8565 (mmt) cc_final: 0.8148 (mmt) outliers start: 20 outliers final: 17 residues processed: 117 average time/residue: 0.1636 time to fit residues: 26.6882 Evaluate side-chains 122 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 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 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU 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: 0.7980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1409 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= 0.194 Angle : 0.499 7.020 9566 Z= 0.254 Chirality : 0.039 0.156 1114 Planarity : 0.004 0.060 1216 Dihedral : 4.027 34.568 1010 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.46 % Allowed : 14.06 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.82 (0.23), residues: 508 sheet: 0.79 (0.73), residues: 53 loop : -1.24 (0.34), residues: 340 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 0.016 0.001 PHE i 225 TYR 0.010 0.001 TYR b 35 ARG 0.007 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 122 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.820 Fit side-chains REVERT: b 317 GLU cc_start: 0.8466 (tt0) cc_final: 0.8264 (tt0) REVERT: i 153 ASP cc_start: 0.8820 (t0) cc_final: 0.8149 (t0) REVERT: i 240 MET cc_start: 0.8597 (mmt) cc_final: 0.8167 (mmt) outliers start: 17 outliers final: 17 residues processed: 111 average time/residue: 0.1518 time to fit residues: 23.9642 Evaluate side-chains 121 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 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 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 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 0.2980 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1448 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= 0.178 Angle : 0.490 7.026 9566 Z= 0.249 Chirality : 0.038 0.152 1114 Planarity : 0.004 0.059 1216 Dihedral : 4.032 35.645 1010 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.61 % Allowed : 13.77 % 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: 1.91 (0.30), residues: 901 helix: 2.86 (0.23), residues: 506 sheet: 0.82 (0.74), residues: 53 loop : -1.25 (0.34), residues: 342 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 0.014 0.001 PHE i 225 TYR 0.009 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 120 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.846 Fit side-chains REVERT: i 153 ASP cc_start: 0.8822 (t0) cc_final: 0.8141 (t0) REVERT: i 240 MET cc_start: 0.8589 (mmt) cc_final: 0.8140 (mmt) outliers start: 18 outliers final: 18 residues processed: 108 average time/residue: 0.1519 time to fit residues: 23.5253 Evaluate side-chains 120 residues out of total 815 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 2 residue 79 ILE Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 136 CYS Chi-restraints excluded: chain i residue 156 ASN Chi-restraints excluded: chain i residue 184 ASP Chi-restraints excluded: chain i residue 208 LEU Chi-restraints excluded: chain i residue 257 LEU Chi-restraints excluded: chain i residue 313 ASP Chi-restraints excluded: chain i residue 355 MET Chi-restraints excluded: chain u residue 14 THR Chi-restraints excluded: chain u residue 66 THR Chi-restraints excluded: chain u residue 67 LEU 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: 4.9990 chunk 19 optimal weight: 0.0060 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.130177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.110838 restraints weight = 9409.859| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.47 r_work: 0.2950 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7044 Z= 0.164 Angle : 0.483 6.997 9566 Z= 0.246 Chirality : 0.038 0.152 1114 Planarity : 0.004 0.059 1216 Dihedral : 3.993 36.269 1010 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.61 % Allowed : 13.77 % 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: 1.98 (0.30), residues: 901 helix: 2.87 (0.23), residues: 509 sheet: 0.89 (0.74), residues: 53 loop : -1.19 (0.35), residues: 339 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 0.017 0.001 PHE i 225 TYR 0.010 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: 1704.80 seconds wall clock time: 31 minutes 3.06 seconds (1863.06 seconds total)