Starting phenix.real_space_refine on Sun Apr 7 12:41:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9x_31829/04_2024/7v9x_31829.pdb" } resolution = 2.82 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= 0.005 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 210 5.49 5 S 23 5.16 5 C 5946 2.51 5 N 1901 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 285": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10550 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Time building chain proxies: 6.55, per 1000 atoms: 0.62 Number of scatterers: 10550 At special positions: 0 Unit cell: (94.35, 129.2, 155.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 210 15.00 O 2470 8.00 N 1901 7.00 C 5946 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: 5.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 8 sheets defined 60.5% alpha, 10.9% beta 64 base pairs and 116 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.633A pdb=" N LEU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 10 " --> pdb=" O TYR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 44 removed outlier: 3.581A pdb=" N TYR A 42 " --> pdb=" O ARG A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.733A pdb=" N LEU A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.691A pdb=" N LEU A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.756A pdb=" N VAL A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 154 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 188 removed outlier: 4.625A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 removed outlier: 3.606A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.655A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'C' and resid 8 through 19 removed outlier: 3.766A pdb=" N GLN C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 19 " --> pdb=" O GLY C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 213 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 236 through 250 Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.575A pdb=" N ARG C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.937A pdb=" N ASN B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 15 " --> pdb=" O ARG B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.615A pdb=" N LEU B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 123 through 127 Processing helix chain 'B' and resid 128 through 139 removed outlier: 4.060A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 188 removed outlier: 4.232A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.664A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 256 through 273 removed outlier: 3.619A pdb=" N TYR B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.679A pdb=" N LYS B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 removed outlier: 3.643A pdb=" N ARG A 63 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 256 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.979A pdb=" N ARG B 63 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 226 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 191 through 194 removed outlier: 3.543A pdb=" N PHE B 114 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 242 through 243 332 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 161 hydrogen bonds 290 hydrogen bond angles 0 basepair planarities 64 basepair parallelities 116 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 5.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1841 1.33 - 1.45: 3746 1.45 - 1.57: 5159 1.57 - 1.69: 410 1.69 - 1.81: 34 Bond restraints: 11190 Sorted by residual: bond pdb=" C3' DG D 73 " pdb=" O3' DG D 73 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" C3' DC D 3 " pdb=" O3' DC D 3 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" C3' DG G 73 " pdb=" O3' DG G 73 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" C3' A E 66 " pdb=" O3' A E 66 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.26e+00 bond pdb=" CB TRP B 284 " pdb=" CG TRP B 284 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.24e+00 ... (remaining 11185 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.31: 1354 106.31 - 113.24: 6181 113.24 - 120.17: 4162 120.17 - 127.10: 3841 127.10 - 134.04: 513 Bond angle restraints: 16051 Sorted by residual: angle pdb=" CB MET C 287 " pdb=" CG MET C 287 " pdb=" SD MET C 287 " ideal model delta sigma weight residual 112.70 102.20 10.50 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C3' A E 66 " pdb=" O3' A E 66 " pdb=" P U E 67 " ideal model delta sigma weight residual 120.20 125.43 -5.23 1.50e+00 4.44e-01 1.22e+01 angle pdb=" CA MET C 287 " pdb=" CB MET C 287 " pdb=" CG MET C 287 " ideal model delta sigma weight residual 114.10 120.41 -6.31 2.00e+00 2.50e-01 9.95e+00 angle pdb=" C3' C E 8 " pdb=" O3' C E 8 " pdb=" P C E 9 " ideal model delta sigma weight residual 120.20 124.82 -4.62 1.50e+00 4.44e-01 9.50e+00 angle pdb=" C3' A H 66 " pdb=" O3' A H 66 " pdb=" P U H 67 " ideal model delta sigma weight residual 120.20 124.34 -4.14 1.50e+00 4.44e-01 7.61e+00 ... (remaining 16046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.67: 6105 35.67 - 71.33: 642 71.33 - 107.00: 37 107.00 - 142.67: 5 142.67 - 178.33: 17 Dihedral angle restraints: 6806 sinusoidal: 4581 harmonic: 2225 Sorted by residual: dihedral pdb=" O4' U H 68 " pdb=" C1' U H 68 " pdb=" N1 U H 68 " pdb=" C2 U H 68 " ideal model delta sinusoidal sigma weight residual 200.00 23.34 176.66 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U E 68 " pdb=" C1' U E 68 " pdb=" N1 U E 68 " pdb=" C2 U E 68 " ideal model delta sinusoidal sigma weight residual 200.00 43.99 156.01 1 1.50e+01 4.44e-03 8.16e+01 dihedral pdb=" O4' C H 65 " pdb=" C1' C H 65 " pdb=" N1 C H 65 " pdb=" C2 C H 65 " ideal model delta sinusoidal sigma weight residual 200.00 71.06 128.94 1 1.50e+01 4.44e-03 6.95e+01 ... (remaining 6803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1466 0.040 - 0.079: 342 0.079 - 0.119: 87 0.119 - 0.159: 17 0.159 - 0.198: 4 Chirality restraints: 1916 Sorted by residual: chirality pdb=" C3' A E 66 " pdb=" C4' A E 66 " pdb=" O3' A E 66 " pdb=" C2' A E 66 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" C1' C H 65 " pdb=" O4' C H 65 " pdb=" C2' C H 65 " pdb=" N1 C H 65 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" C1' C E 65 " pdb=" O4' C E 65 " pdb=" C2' C E 65 " pdb=" N1 C E 65 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1913 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A E 17 " -0.023 2.00e-02 2.50e+03 1.08e-02 3.19e+00 pdb=" N9 A E 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A E 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A E 17 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A E 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A E 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A E 17 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A E 17 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A E 17 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 80 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.62e+00 pdb=" C LEU B 80 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU B 80 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 81 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA D 6 " -0.018 2.00e-02 2.50e+03 8.09e-03 1.80e+00 pdb=" N9 DA D 6 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA D 6 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA D 6 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA D 6 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA D 6 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA D 6 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA D 6 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA D 6 " 0.002 2.00e-02 2.50e+03 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1933 2.77 - 3.30: 8918 3.30 - 3.84: 18963 3.84 - 4.37: 23081 4.37 - 4.90: 35214 Nonbonded interactions: 88109 Sorted by model distance: nonbonded pdb=" OD1 ASN B 8 " pdb=" NH2 ARG B 11 " model vdw 2.241 2.520 nonbonded pdb=" O TYR C 211 " pdb=" NH2 ARG B 31 " model vdw 2.254 2.520 nonbonded pdb=" O LEU A 39 " pdb=" OG1 THR A 43 " model vdw 2.260 2.440 nonbonded pdb=" NZ LYS B 60 " pdb=" OE2 GLU B 121 " model vdw 2.274 2.520 nonbonded pdb=" O PHE B 287 " pdb=" OG SER B 290 " model vdw 2.276 2.440 ... (remaining 88104 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } 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: 1.020 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: 5.120 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.780 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 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:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11190 Z= 0.280 Angle : 0.626 10.501 16051 Z= 0.335 Chirality : 0.039 0.198 1916 Planarity : 0.004 0.045 1259 Dihedral : 24.075 178.334 5372 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.17 (0.30), residues: 750 helix: 0.89 (0.27), residues: 394 sheet: 1.50 (0.64), residues: 62 loop : -1.26 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 284 HIS 0.005 0.001 HIS B 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.005 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.795 Fit side-chains REVERT: A 45 ASP cc_start: 0.7618 (m-30) cc_final: 0.7343 (m-30) REVERT: A 231 LYS cc_start: 0.6377 (mptt) cc_final: 0.6075 (mptt) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 1.3106 time to fit residues: 125.7221 Evaluate side-chains 63 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 chunk 38 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 ASN B 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.252 Angle : 0.599 8.903 16051 Z= 0.320 Chirality : 0.038 0.195 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.277 178.739 3825 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.47 % Allowed : 8.21 % Favored : 90.32 % 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: 0.32 (0.30), residues: 750 helix: 1.06 (0.26), residues: 402 sheet: 2.03 (0.62), residues: 58 loop : -1.41 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.007 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 64 time to evaluate : 0.834 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7635 (m-30) cc_final: 0.7349 (m-30) REVERT: A 119 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: A 231 LYS cc_start: 0.6466 (mptt) cc_final: 0.6230 (mptt) REVERT: C 239 ILE cc_start: 0.8247 (mp) cc_final: 0.8032 (tt) REVERT: B 251 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7150 (mm-30) REVERT: B 282 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7631 (ttp-170) outliers start: 10 outliers final: 5 residues processed: 68 average time/residue: 1.2519 time to fit residues: 92.4354 Evaluate side-chains 70 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.231 Angle : 0.584 9.626 16051 Z= 0.311 Chirality : 0.037 0.194 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.217 179.134 3825 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 10.70 % Favored : 87.68 % 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: 0.42 (0.30), residues: 750 helix: 1.18 (0.26), residues: 402 sheet: 2.03 (0.61), residues: 58 loop : -1.42 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.012 0.001 TYR B 179 ARG 0.005 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 66 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7536 (m-30) cc_final: 0.7290 (m-30) REVERT: A 119 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: A 231 LYS cc_start: 0.6439 (mptt) cc_final: 0.6180 (mptt) REVERT: B 251 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7160 (mm-30) REVERT: B 282 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7640 (ttp-170) outliers start: 11 outliers final: 6 residues processed: 69 average time/residue: 1.2765 time to fit residues: 95.2826 Evaluate side-chains 73 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 43 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.256 Angle : 0.598 10.149 16051 Z= 0.318 Chirality : 0.038 0.196 1916 Planarity : 0.004 0.037 1259 Dihedral : 26.206 179.199 3825 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.05 % Allowed : 11.58 % Favored : 86.36 % 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: 0.41 (0.30), residues: 750 helix: 1.21 (0.27), residues: 400 sheet: 1.99 (0.62), residues: 58 loop : -1.46 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.005 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 66 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7536 (m-30) cc_final: 0.7292 (m-30) REVERT: A 119 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: A 231 LYS cc_start: 0.6457 (mptt) cc_final: 0.6192 (mptt) REVERT: B 251 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: B 282 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7684 (ttp-170) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 1.2642 time to fit residues: 97.1709 Evaluate side-chains 76 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 67 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11190 Z= 0.291 Angle : 0.615 10.449 16051 Z= 0.328 Chirality : 0.039 0.198 1916 Planarity : 0.004 0.039 1259 Dihedral : 26.237 179.950 3825 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 12.32 % Favored : 85.48 % 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: 0.31 (0.30), residues: 750 helix: 1.14 (0.27), residues: 400 sheet: 1.93 (0.62), residues: 58 loop : -1.52 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 284 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.014 0.001 TYR B 179 ARG 0.004 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 69 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7511 (m-30) cc_final: 0.7280 (m-30) REVERT: A 119 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: A 231 LYS cc_start: 0.6460 (mptt) cc_final: 0.6197 (mptt) REVERT: B 251 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7196 (mm-30) REVERT: B 282 ARG cc_start: 0.8050 (ttm110) cc_final: 0.7689 (ttp-170) outliers start: 15 outliers final: 8 residues processed: 75 average time/residue: 1.2066 time to fit residues: 98.0722 Evaluate side-chains 75 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.8178 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11190 Z= 0.282 Angle : 0.612 10.361 16051 Z= 0.325 Chirality : 0.039 0.195 1916 Planarity : 0.004 0.039 1259 Dihedral : 26.232 179.901 3825 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 13.64 % Favored : 84.16 % 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: 0.26 (0.30), residues: 750 helix: 1.12 (0.27), residues: 400 sheet: 1.18 (0.58), residues: 68 loop : -1.49 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.013 0.001 TYR B 179 ARG 0.003 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7527 (m-30) cc_final: 0.7294 (m-30) REVERT: A 119 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7988 (m-30) REVERT: A 231 LYS cc_start: 0.6492 (mptt) cc_final: 0.6212 (mptt) REVERT: B 251 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: B 282 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7730 (ttp-170) outliers start: 15 outliers final: 7 residues processed: 73 average time/residue: 1.3193 time to fit residues: 103.9658 Evaluate side-chains 74 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 0.0670 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.5722 ------------------------------------------------------------------------------- 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: 0.8165 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11190 Z= 0.220 Angle : 0.593 10.329 16051 Z= 0.316 Chirality : 0.038 0.193 1916 Planarity : 0.004 0.037 1259 Dihedral : 26.221 179.976 3825 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.20 % Allowed : 13.78 % Favored : 84.02 % 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: 0.37 (0.30), residues: 750 helix: 1.17 (0.27), residues: 400 sheet: 1.95 (0.63), residues: 58 loop : -1.47 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.012 0.001 TYR B 179 ARG 0.003 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 65 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7505 (m-30) cc_final: 0.7278 (m-30) REVERT: A 119 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: A 231 LYS cc_start: 0.6458 (mptt) cc_final: 0.6180 (mptt) REVERT: C 241 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7629 (mmp80) REVERT: B 251 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: B 282 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7724 (ttp-170) outliers start: 15 outliers final: 5 residues processed: 70 average time/residue: 1.2481 time to fit residues: 94.2990 Evaluate side-chains 72 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8150 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11190 Z= 0.180 Angle : 0.580 10.720 16051 Z= 0.309 Chirality : 0.037 0.192 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.210 179.880 3825 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.76 % Allowed : 14.37 % Favored : 83.87 % 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: 0.47 (0.31), residues: 750 helix: 1.26 (0.27), residues: 400 sheet: 2.01 (0.64), residues: 58 loop : -1.42 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.014 0.001 TYR C 218 ARG 0.003 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7478 (m-30) cc_final: 0.7253 (m-30) REVERT: A 62 MET cc_start: 0.6730 (pmm) cc_final: 0.5456 (ttp) REVERT: A 119 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: A 231 LYS cc_start: 0.6503 (mptt) cc_final: 0.6221 (mptt) REVERT: B 251 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7209 (mm-30) REVERT: B 282 ARG cc_start: 0.8030 (ttm110) cc_final: 0.7676 (ttp-170) outliers start: 12 outliers final: 4 residues processed: 74 average time/residue: 1.3098 time to fit residues: 104.6111 Evaluate side-chains 72 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 0.0970 chunk 86 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11190 Z= 0.154 Angle : 0.574 10.124 16051 Z= 0.304 Chirality : 0.036 0.207 1916 Planarity : 0.003 0.033 1259 Dihedral : 26.185 179.620 3825 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.17 % Allowed : 14.81 % Favored : 84.02 % 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: 0.51 (0.31), residues: 750 helix: 1.27 (0.27), residues: 400 sheet: 2.11 (0.64), residues: 58 loop : -1.38 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 78 HIS 0.004 0.001 HIS C 16 PHE 0.011 0.001 PHE B 92 TYR 0.019 0.001 TYR C 218 ARG 0.003 0.000 ARG C 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7449 (m-30) cc_final: 0.7243 (m-30) REVERT: A 62 MET cc_start: 0.6743 (pmm) cc_final: 0.5855 (ppp) REVERT: A 119 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 231 LYS cc_start: 0.6485 (mptt) cc_final: 0.6202 (mptt) REVERT: B 251 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: B 282 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7660 (ttp-170) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 1.3709 time to fit residues: 101.6338 Evaluate side-chains 75 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11190 Z= 0.270 Angle : 0.603 10.456 16051 Z= 0.320 Chirality : 0.038 0.196 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.182 179.631 3825 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.61 % Allowed : 14.66 % Favored : 83.72 % 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: 0.44 (0.31), residues: 750 helix: 1.22 (0.27), residues: 402 sheet: 1.29 (0.60), residues: 68 loop : -1.34 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS A 280 PHE 0.013 0.002 PHE B 92 TYR 0.014 0.001 TYR C 218 ARG 0.003 0.000 ARG C 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1500 Ramachandran restraints generated. 750 Oldfield, 0 Emsley, 750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 70 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7517 (m-30) cc_final: 0.7287 (m-30) REVERT: A 119 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: A 231 LYS cc_start: 0.6486 (mptt) cc_final: 0.6204 (mptt) REVERT: B 251 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: B 282 ARG cc_start: 0.8075 (ttm110) cc_final: 0.7708 (ttp-170) outliers start: 11 outliers final: 5 residues processed: 75 average time/residue: 1.4919 time to fit residues: 119.9881 Evaluate side-chains 74 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 300 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 240 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.147064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.099183 restraints weight = 14606.038| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.77 r_work: 0.3158 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11190 Z= 0.189 Angle : 0.595 11.360 16051 Z= 0.315 Chirality : 0.037 0.193 1916 Planarity : 0.004 0.036 1259 Dihedral : 26.177 179.769 3825 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.17 % Allowed : 15.40 % Favored : 83.43 % 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: 0.52 (0.31), residues: 750 helix: 1.29 (0.27), residues: 402 sheet: 1.29 (0.60), residues: 68 loop : -1.33 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 78 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE B 92 TYR 0.013 0.001 TYR C 218 ARG 0.006 0.000 ARG C 246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.04 seconds wall clock time: 52 minutes 56.80 seconds (3176.80 seconds total)