Starting phenix.real_space_refine on Sat Jan 20 01:34:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzj_41760/01_2024/8tzj_41760_updated.pdb" } resolution = 3.51 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= 0.001 sd= 0.028 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 26 5.16 5 C 4210 2.51 5 N 1184 2.21 5 O 1148 1.98 5 H 6772 0.53 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-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13346 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3495 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3151 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "D" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 3150 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 4, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.58, per 1000 atoms: 0.49 Number of scatterers: 13346 At special positions: 0 Unit cell: (70.2, 83.16, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 26 16.00 P 4 15.00 Mg 2 11.99 O 1148 8.00 N 1184 7.00 C 4210 6.00 H 6772 1.00 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: 10.29 Conformation dependent library (CDL) restraints added in 1.4 seconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 4 sheets defined 60.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.37 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 removed outlier: 3.504A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.851A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 179 through 195 removed outlier: 4.041A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'B' and resid 50 through 58 removed outlier: 3.504A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 89 removed outlier: 3.851A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 120 through 134 Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 149 through 161 Processing helix chain 'B' and resid 179 through 195 removed outlier: 4.041A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'C' and resid 32 through 48 removed outlier: 4.331A pdb=" N TRP C 48 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 84 removed outlier: 3.739A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix Processing helix chain 'C' and resid 188 through 228 removed outlier: 3.836A pdb=" N ALA C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 243 through 286 Proline residue: C 249 - end of helix removed outlier: 4.135A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.676A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 316 " --> pdb=" O GLY C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 49 removed outlier: 4.254A pdb=" N TRP D 48 " --> pdb=" O PHE D 44 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 84 removed outlier: 3.870A pdb=" N LEU D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR D 57 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 58 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 188 through 228 removed outlier: 3.509A pdb=" N ASP D 193 " --> pdb=" O PHE D 189 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 243 through 287 Proline residue: D 249 - end of helix removed outlier: 4.049A pdb=" N GLY D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 326 removed outlier: 3.697A pdb=" N ALA D 316 " --> pdb=" O GLY D 312 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.661A pdb=" N LEU A 167 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL A 93 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 169 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 198 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A 170 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 200 " --> pdb=" O ALA A 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'B' and resid 90 through 93 removed outlier: 6.661A pdb=" N LEU B 167 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N VAL B 93 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 169 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 198 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA B 170 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 200 " --> pdb=" O ALA B 170 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 355 hydrogen bonds defined for protein. 1053 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: 4.39 Time building geometry restraints manager: 10.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6766 1.03 - 1.23: 28 1.23 - 1.42: 2664 1.42 - 1.61: 3946 1.61 - 1.81: 52 Bond restraints: 13456 Sorted by residual: bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.393 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.447 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C5 ADP B 302 " pdb=" C6 ADP B 302 " ideal model delta sigma weight residual 1.490 1.415 0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 13451 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.62: 269 106.62 - 113.59: 16057 113.59 - 120.56: 4824 120.56 - 127.53: 3165 127.53 - 134.50: 62 Bond angle restraints: 24377 Sorted by residual: angle pdb=" N LYS B 50 " pdb=" CA LYS B 50 " pdb=" C LYS B 50 " ideal model delta sigma weight residual 111.07 115.88 -4.81 1.07e+00 8.73e-01 2.02e+01 angle pdb=" N LYS A 50 " pdb=" CA LYS A 50 " pdb=" C LYS A 50 " ideal model delta sigma weight residual 111.07 115.85 -4.78 1.07e+00 8.73e-01 2.00e+01 angle pdb=" N GLN B 25 " pdb=" CA GLN B 25 " pdb=" C GLN B 25 " ideal model delta sigma weight residual 108.52 115.37 -6.85 1.63e+00 3.76e-01 1.76e+01 angle pdb=" N GLN A 25 " pdb=" CA GLN A 25 " pdb=" C GLN A 25 " ideal model delta sigma weight residual 108.52 115.34 -6.82 1.63e+00 3.76e-01 1.75e+01 angle pdb=" CA ALA A 48 " pdb=" C ALA A 48 " pdb=" N GLY A 49 " ideal model delta sigma weight residual 117.19 122.78 -5.59 1.50e+00 4.44e-01 1.39e+01 ... (remaining 24372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.57: 5936 26.57 - 53.14: 148 53.14 - 79.71: 12 79.71 - 106.28: 4 106.28 - 132.85: 2 Dihedral angle restraints: 6102 sinusoidal: 3317 harmonic: 2785 Sorted by residual: dihedral pdb=" O2A ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PA ADP A 302 " pdb=" PB ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.85 -132.85 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 72.82 -132.82 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 45.65 -105.66 1 2.00e+01 2.50e-03 3.05e+01 ... (remaining 6099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 920 0.051 - 0.103: 122 0.103 - 0.154: 26 0.154 - 0.206: 2 0.206 - 0.257: 4 Chirality restraints: 1074 Sorted by residual: chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.77 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2' ADP B 302 " pdb=" C1' ADP B 302 " pdb=" C3' ADP B 302 " pdb=" O2' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1071 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 18 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C LYS A 18 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS A 18 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 19 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 18 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C LYS B 18 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS B 18 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA B 19 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 44 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C GLY A 44 " 0.030 2.00e-02 2.50e+03 pdb=" O GLY A 44 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 45 " -0.010 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 240 2.11 - 2.73: 24172 2.73 - 3.36: 36972 3.36 - 3.98: 44671 3.98 - 4.60: 72649 Nonbonded interactions: 178704 Sorted by model distance: nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.490 1.850 nonbonded pdb=" HD1 HIS C 36 " pdb=" OH TYR C 252 " model vdw 1.537 1.850 nonbonded pdb=" HE2 PHE B 13 " pdb="HD11 LEU B 53 " model vdw 1.550 2.270 nonbonded pdb=" HE2 PHE A 13 " pdb="HD11 LEU A 53 " model vdw 1.551 2.270 nonbonded pdb=" O ALA D 284 " pdb=" H ASP D 288 " model vdw 1.639 1.850 ... (remaining 178699 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' and (resid 9 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name OG or name H or name HA or name HB2 or name HB3)) \ or resid 52 through 228 or resid 301 through 302)) } ncs_group { reference = (chain 'C' and (resid 27 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE \ 2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name H \ E1)) or resid 37 through 330)) selection = chain 'D' } 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 group one per residue 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: 1.060 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: 0.200 Extract box with map and model: 4.150 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 45.670 Find NCS groups from input model: 0.530 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.004 0.097 6684 Z= 0.286 Angle : 0.670 10.288 9050 Z= 0.341 Chirality : 0.040 0.257 1074 Planarity : 0.003 0.026 1130 Dihedral : 12.126 132.849 2450 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.15 % Allowed : 3.24 % Favored : 96.62 % 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: 2.16 (0.30), residues: 834 helix: 2.73 (0.23), residues: 508 sheet: -0.71 (0.77), residues: 56 loop : -0.67 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 48 HIS 0.002 0.001 HIS C 36 PHE 0.010 0.001 PHE C 32 TYR 0.008 0.001 TYR C 250 ARG 0.005 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8343 (mttt) cc_final: 0.8130 (mttm) REVERT: C 212 MET cc_start: 0.7410 (tpp) cc_final: 0.7209 (tpt) REVERT: C 302 LEU cc_start: 0.8034 (mt) cc_final: 0.7659 (tt) REVERT: D 76 LYS cc_start: 0.8437 (tttt) cc_final: 0.8229 (tptt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.6998 time to fit residues: 136.6056 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7751 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 6684 Z= 0.300 Angle : 0.593 6.517 9050 Z= 0.295 Chirality : 0.037 0.151 1074 Planarity : 0.004 0.033 1130 Dihedral : 8.561 123.536 940 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.88 % Allowed : 8.09 % Favored : 91.03 % 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: 1.99 (0.29), residues: 834 helix: 2.49 (0.22), residues: 514 sheet: -1.01 (0.72), residues: 66 loop : -0.49 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 256 HIS 0.017 0.001 HIS A 97 PHE 0.015 0.002 PHE C 215 TYR 0.013 0.001 TYR C 250 ARG 0.004 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8381 (mttt) cc_final: 0.8148 (mtmt) REVERT: B 39 MET cc_start: 0.8224 (ttt) cc_final: 0.8009 (ttp) REVERT: C 302 LEU cc_start: 0.8167 (mt) cc_final: 0.7922 (tt) REVERT: D 76 LYS cc_start: 0.8341 (tttt) cc_final: 0.8070 (tptt) REVERT: D 300 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7619 (mt-10) outliers start: 6 outliers final: 4 residues processed: 101 average time/residue: 0.5110 time to fit residues: 65.2961 Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 87 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 81 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN B 221 ASN ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6684 Z= 0.208 Angle : 0.527 5.996 9050 Z= 0.259 Chirality : 0.036 0.149 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.173 129.699 940 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 9.26 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.30), residues: 834 helix: 2.54 (0.22), residues: 514 sheet: -1.01 (0.73), residues: 66 loop : -0.44 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 256 HIS 0.012 0.001 HIS A 97 PHE 0.010 0.001 PHE C 215 TYR 0.011 0.001 TYR C 250 ARG 0.002 0.000 ARG C 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 MET cc_start: 0.8308 (ttt) cc_final: 0.8075 (ttp) REVERT: C 302 LEU cc_start: 0.8034 (mt) cc_final: 0.7811 (tt) REVERT: D 76 LYS cc_start: 0.8264 (tttt) cc_final: 0.8027 (tptt) outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.5274 time to fit residues: 65.4451 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 72 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6684 Z= 0.182 Angle : 0.511 6.202 9050 Z= 0.248 Chirality : 0.035 0.147 1074 Planarity : 0.004 0.056 1130 Dihedral : 8.091 138.435 940 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.18 % Allowed : 9.85 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.30), residues: 834 helix: 2.70 (0.22), residues: 514 sheet: -1.03 (0.73), residues: 66 loop : -0.34 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.010 0.001 HIS A 97 PHE 0.012 0.001 PHE D 189 TYR 0.011 0.001 TYR C 250 ARG 0.005 0.000 ARG D 223 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 GLU cc_start: 0.7847 (tp30) cc_final: 0.7608 (tp30) REVERT: D 76 LYS cc_start: 0.8289 (tttt) cc_final: 0.8036 (tptt) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.5350 time to fit residues: 66.8772 Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.0040 chunk 33 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6684 Z= 0.248 Angle : 0.534 6.091 9050 Z= 0.261 Chirality : 0.036 0.147 1074 Planarity : 0.003 0.030 1130 Dihedral : 8.352 151.047 940 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.62 % Allowed : 10.29 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.30), residues: 834 helix: 2.64 (0.22), residues: 514 sheet: -1.12 (0.72), residues: 66 loop : -0.39 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.007 0.001 HIS A 97 PHE 0.011 0.001 PHE C 215 TYR 0.013 0.001 TYR C 250 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 99 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8313 (tttt) cc_final: 0.8062 (tptt) outliers start: 11 outliers final: 9 residues processed: 96 average time/residue: 0.5060 time to fit residues: 61.6429 Evaluate side-chains 93 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6684 Z= 0.199 Angle : 0.520 6.128 9050 Z= 0.251 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.053 1130 Dihedral : 8.418 156.960 940 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.62 % Allowed : 10.88 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.30), residues: 834 helix: 2.73 (0.23), residues: 514 sheet: -1.09 (0.72), residues: 66 loop : -0.31 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 PHE 0.010 0.001 PHE C 215 TYR 0.012 0.001 TYR A 215 ARG 0.006 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8314 (tttt) cc_final: 0.8063 (tptt) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.4978 time to fit residues: 60.6816 Evaluate side-chains 90 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6684 Z= 0.270 Angle : 0.544 6.050 9050 Z= 0.267 Chirality : 0.036 0.145 1074 Planarity : 0.003 0.043 1130 Dihedral : 8.647 164.455 940 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.62 % Allowed : 11.76 % Favored : 86.62 % 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: 2.22 (0.30), residues: 834 helix: 2.60 (0.22), residues: 522 sheet: -1.10 (0.72), residues: 66 loop : -0.28 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.011 0.001 PHE C 215 TYR 0.013 0.001 TYR C 250 ARG 0.007 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 98 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8314 (tttt) cc_final: 0.8077 (tptt) outliers start: 11 outliers final: 10 residues processed: 95 average time/residue: 0.4912 time to fit residues: 59.6937 Evaluate side-chains 97 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 7 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6684 Z= 0.184 Angle : 0.519 6.208 9050 Z= 0.250 Chirality : 0.035 0.146 1074 Planarity : 0.003 0.049 1130 Dihedral : 8.778 171.663 940 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.18 % Allowed : 12.21 % Favored : 86.62 % 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: 2.43 (0.31), residues: 834 helix: 2.75 (0.23), residues: 522 sheet: -1.10 (0.72), residues: 66 loop : -0.11 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.006 0.001 HIS A 97 PHE 0.013 0.001 PHE C 291 TYR 0.011 0.001 TYR A 215 ARG 0.007 0.000 ARG B 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8312 (tttt) cc_final: 0.8066 (tptt) outliers start: 8 outliers final: 7 residues processed: 93 average time/residue: 0.4916 time to fit residues: 58.5014 Evaluate side-chains 94 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 48 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7789 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6684 Z= 0.175 Angle : 0.512 6.217 9050 Z= 0.246 Chirality : 0.035 0.145 1074 Planarity : 0.004 0.081 1130 Dihedral : 8.974 174.751 940 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.32 % Allowed : 11.62 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.31), residues: 834 helix: 2.88 (0.23), residues: 522 sheet: -1.04 (0.73), residues: 66 loop : -0.04 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.011 0.001 PHE C 291 TYR 0.011 0.001 TYR A 215 ARG 0.014 0.000 ARG C 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 96 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 76 LYS cc_start: 0.8319 (tttt) cc_final: 0.8092 (tptt) outliers start: 9 outliers final: 7 residues processed: 93 average time/residue: 0.4960 time to fit residues: 59.1116 Evaluate side-chains 91 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6684 Z= 0.275 Angle : 0.548 6.081 9050 Z= 0.268 Chirality : 0.036 0.146 1074 Planarity : 0.003 0.023 1130 Dihedral : 8.871 176.111 940 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.32 % Allowed : 11.62 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.31), residues: 834 helix: 2.80 (0.23), residues: 520 sheet: -1.09 (0.73), residues: 66 loop : 0.03 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.011 0.001 PHE C 215 TYR 0.013 0.001 TYR D 250 ARG 0.007 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Evaluate side-chains 95 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 104 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8129 (t) REVERT: D 76 LYS cc_start: 0.8372 (tttt) cc_final: 0.8136 (tptt) outliers start: 9 outliers final: 8 residues processed: 93 average time/residue: 0.5262 time to fit residues: 62.6403 Evaluate side-chains 95 residues out of total 704 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain B residue 104 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 291 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.122397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103476 restraints weight = 28017.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107980 restraints weight = 14124.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110970 restraints weight = 8784.762| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6684 Z= 0.173 Angle : 0.516 6.167 9050 Z= 0.248 Chirality : 0.035 0.146 1074 Planarity : 0.004 0.063 1130 Dihedral : 8.737 173.961 940 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.18 % Allowed : 11.62 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.31), residues: 834 helix: 2.88 (0.23), residues: 522 sheet: -1.08 (0.72), residues: 66 loop : -0.01 (0.42), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.005 0.001 HIS A 97 PHE 0.010 0.001 PHE C 291 TYR 0.011 0.001 TYR A 215 ARG 0.010 0.000 ARG B 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.13 seconds wall clock time: 55 minutes 22.15 seconds (3322.15 seconds total)