Starting phenix.real_space_refine on Tue Sep 24 14:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o6p_12739/09_2024/7o6p_12739.cif" } resolution = 2.04 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= 0.004 sd= 0.042 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5014 2.51 5 N 1451 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8276 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2010 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1913 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 256, 1913 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 1 bond proxies already assigned to first conformer: 1837 Chain: "B" Number of atoms: 1980 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 255, 1905 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 255, 1905 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 bond proxies already assigned to first conformer: 1855 Chain: "C" Number of atoms: 1991 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1901 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 254, 1901 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain breaks: 1 bond proxies already assigned to first conformer: 1833 Chain: "D" Number of atoms: 2027 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 257, 1919 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 257, 1919 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 bond proxies already assigned to first conformer: 1831 Chain: "A" Number of atoms: 68 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} Chain: "B" Number of atoms: 71 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Conformer: "A" Number of residues, atoms: 70, 70 Classifications: {'water': 70} Link IDs: {None: 69} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "D" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Residues with excluded nonbonded symmetry interactions: 43 residue: pdb=" N AARG A 20 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 20 " occ=0.50 residue: pdb=" N ASER A 34 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 34 " occ=0.50 residue: pdb=" N AARG A 40 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 40 " occ=0.50 residue: pdb=" N ALYS A 45 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 45 " occ=0.50 residue: pdb=" N AARG A 84 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 84 " occ=0.50 residue: pdb=" N ALYS A 147 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 147 " occ=0.50 residue: pdb=" N ALYS A 181 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 181 " occ=0.50 residue: pdb=" N AARG A 225 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 225 " occ=0.50 residue: pdb=" N AGLU A 238 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A 238 " occ=0.50 residue: pdb=" N AARG A 257 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 257 " occ=0.50 residue: pdb=" N ALEU B 37 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU B 37 " occ=0.50 residue: pdb=" N ALYS B 83 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 83 " occ=0.50 ... (remaining 31 not shown) Time building chain proxies: 8.94, per 1000 atoms: 1.08 Number of scatterers: 8276 At special positions: 0 Unit cell: (81.536, 93.184, 79.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1759 8.00 N 1451 7.00 C 5014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 53.9% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 30 through 42 removed outlier: 3.507A pdb=" N ASER A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.558A pdb=" N CYS A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 64 " --> pdb=" O CYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 129 through 147 removed outlier: 3.726A pdb=" N ILE A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Proline residue: A 145 - end of helix Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 166 through 188 Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 240 through 253 removed outlier: 3.610A pdb=" N VAL A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 257 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 52 through 64 removed outlier: 3.842A pdb=" N GLN B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.727A pdb=" N ILE B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Proline residue: B 145 - end of helix Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 166 through 188 Processing helix chain 'B' and resid 221 through 231 Processing helix chain 'B' and resid 240 through 253 removed outlier: 3.606A pdb=" N VAL B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 52 through 64 removed outlier: 3.871A pdb=" N ARG C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 94 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 129 through 147 removed outlier: 3.730A pdb=" N ILE C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Proline residue: C 145 - end of helix Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 240 through 253 removed outlier: 3.597A pdb=" N VAL C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'D' and resid 30 through 42 Processing helix chain 'D' and resid 52 through 64 removed outlier: 3.720A pdb=" N GLY D 64 " --> pdb=" O CYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 94 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 129 through 147 removed outlier: 3.732A pdb=" N ILE D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 166 through 188 Processing helix chain 'D' and resid 220 through 231 Processing helix chain 'D' and resid 240 through 253 removed outlier: 3.619A pdb=" N VAL D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 257 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 73 removed outlier: 6.552A pdb=" N VAL A 21 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL A 100 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 23 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N MET A 99 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 154 " --> pdb=" O MET A 99 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 101 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A 262 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 73 removed outlier: 6.537A pdb=" N VAL B 21 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL B 100 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 23 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N MET B 99 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE B 154 " --> pdb=" O MET B 99 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN B 101 " --> pdb=" O ILE B 154 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N MET B 262 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL B 194 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU B 264 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N CYS B 196 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL B 266 " --> pdb=" O CYS B 196 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N SER B 198 " --> pdb=" O VAL B 266 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 73 removed outlier: 6.563A pdb=" N VAL C 21 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 100 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 23 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET C 99 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE C 154 " --> pdb=" O MET C 99 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ASN C 101 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N LEU C 264 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N CYS C 196 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL C 266 " --> pdb=" O CYS C 196 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER C 198 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.558A pdb=" N VAL D 21 " --> pdb=" O ILE D 98 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D 100 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 23 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N MET D 99 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 154 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ASN D 101 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU D 264 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N CYS D 196 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL D 266 " --> pdb=" O CYS D 196 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER D 198 " --> pdb=" O VAL D 266 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1333 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: 2.54 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2778 1.34 - 1.46: 1652 1.46 - 1.58: 3658 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 8168 Sorted by residual: bond pdb=" CB ALYS D 189 " pdb=" CG ALYS D 189 " ideal model delta sigma weight residual 1.520 1.470 0.050 3.00e-02 1.11e+03 2.78e+00 bond pdb=" CA GLN D 52 " pdb=" C GLN D 52 " ideal model delta sigma weight residual 1.532 1.520 0.013 9.60e-03 1.09e+04 1.80e+00 bond pdb=" CG1 ILE D 98 " pdb=" CD1 ILE D 98 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CG1 ILE B 98 " pdb=" CD1 ILE B 98 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CG1 ILE A 98 " pdb=" CD1 ILE A 98 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 ... (remaining 8163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 10294 1.06 - 2.11: 636 2.11 - 3.17: 121 3.17 - 4.23: 23 4.23 - 5.28: 6 Bond angle restraints: 11080 Sorted by residual: angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N SER B 156 " ideal model delta sigma weight residual 117.21 120.45 -3.24 1.42e+00 4.96e-01 5.22e+00 angle pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N SER A 156 " ideal model delta sigma weight residual 117.21 120.45 -3.24 1.42e+00 4.96e-01 5.20e+00 angle pdb=" CA SER C 155 " pdb=" C SER C 155 " pdb=" N SER C 156 " ideal model delta sigma weight residual 117.21 120.43 -3.22 1.42e+00 4.96e-01 5.13e+00 angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" O SER B 155 " ideal model delta sigma weight residual 120.84 117.86 2.98 1.33e+00 5.65e-01 5.01e+00 angle pdb=" C ALA B 256 " pdb=" N BARG B 257 " pdb=" CA BARG B 257 " ideal model delta sigma weight residual 120.38 123.64 -3.26 1.46e+00 4.69e-01 4.99e+00 ... (remaining 11075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 4535 16.21 - 32.42: 316 32.42 - 48.63: 48 48.63 - 64.84: 12 64.84 - 81.05: 5 Dihedral angle restraints: 4916 sinusoidal: 1901 harmonic: 3015 Sorted by residual: dihedral pdb=" CA PRO A 199 " pdb=" C PRO A 199 " pdb=" N TYR A 200 " pdb=" CA TYR A 200 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA PRO C 199 " pdb=" C PRO C 199 " pdb=" N TYR C 200 " pdb=" CA TYR C 200 " ideal model delta harmonic sigma weight residual 180.00 163.86 16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA CYS A 60 " pdb=" C CYS A 60 " pdb=" N GLU A 61 " pdb=" CA GLU A 61 " ideal model delta harmonic sigma weight residual 180.00 163.94 16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 4913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 458 0.027 - 0.054: 446 0.054 - 0.081: 244 0.081 - 0.108: 83 0.108 - 0.135: 33 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CB ILE A 192 " pdb=" CA ILE A 192 " pdb=" CG1 ILE A 192 " pdb=" CG2 ILE A 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CB ILE C 192 " pdb=" CA ILE C 192 " pdb=" CG1 ILE C 192 " pdb=" CG2 ILE C 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CB ILE D 192 " pdb=" CA ILE D 192 " pdb=" CG1 ILE D 192 " pdb=" CG2 ILE D 192 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1261 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 198 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO B 199 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 199 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 199 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 198 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.12e+00 pdb=" N PRO D 199 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 198 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.94e+00 pdb=" N PRO A 199 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 199 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 199 " 0.027 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 247 2.69 - 3.24: 8750 3.24 - 3.80: 14430 3.80 - 4.35: 20153 4.35 - 4.90: 31567 Nonbonded interactions: 75147 Sorted by model distance: nonbonded pdb=" OD2 ASP A 112 " pdb=" O HOH A 301 " model vdw 2.140 3.040 nonbonded pdb=" OD2 ASP D 112 " pdb=" O HOH D 301 " model vdw 2.161 3.040 nonbonded pdb=" OD2 ASP C 112 " pdb=" O HOH C 301 " model vdw 2.168 3.040 nonbonded pdb=" O VAL C 237 " pdb=" O HOH C 302 " model vdw 2.179 3.040 nonbonded pdb=" O VAL A 237 " pdb=" O HOH A 302 " model vdw 2.180 3.040 ... (remaining 75142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'B' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'C' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) selection = (chain 'D' and (resid 13 through 19 or resid 21 through 33 or resid 35 through 3 \ 6 or resid 38 through 39 or resid 41 through 44 or resid 46 through 82 or resid \ 85 through 89 or resid 91 through 116 or resid 118 through 146 or resid 149 thro \ ugh 180 or resid 182 through 188 or resid 190 through 202 or resid 220 through 2 \ 24 or resid 226 through 237 or resid 239 through 256 or resid 258 through 282)) } 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=0.50 max=1.00 mean=0.96 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: 5.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.008 0.050 8168 Z= 0.537 Angle : 0.594 5.284 11080 Z= 0.334 Chirality : 0.049 0.135 1264 Planarity : 0.005 0.052 1468 Dihedral : 11.733 81.046 3002 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.93 % Allowed : 5.10 % Favored : 93.97 % 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: -0.54 (0.23), residues: 1117 helix: -0.01 (0.22), residues: 511 sheet: 0.38 (0.39), residues: 176 loop : -0.96 (0.26), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 221 HIS 0.012 0.002 HIS A 138 PHE 0.016 0.003 PHE C 133 TYR 0.014 0.003 TYR C 200 ARG 0.003 0.001 ARG C 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.863 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 113 average time/residue: 1.8854 time to fit residues: 221.9784 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain D residue 92 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 235 GLN C 235 GLN D 233 ASN D 235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8168 Z= 0.226 Angle : 0.522 9.058 11080 Z= 0.287 Chirality : 0.044 0.146 1264 Planarity : 0.004 0.048 1468 Dihedral : 5.101 55.886 1180 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.35 % Allowed : 9.74 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1117 helix: 1.31 (0.22), residues: 535 sheet: 0.49 (0.37), residues: 180 loop : -0.34 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 221 HIS 0.003 0.001 HIS D 138 PHE 0.011 0.002 PHE C 133 TYR 0.017 0.002 TYR C 169 ARG 0.006 0.001 ARG B 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7743 (tttt) REVERT: D 92 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7701 (tttt) outliers start: 3 outliers final: 0 residues processed: 82 average time/residue: 1.6398 time to fit residues: 141.5027 Evaluate side-chains 74 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain D residue 92 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN D 233 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8168 Z= 0.203 Angle : 0.476 8.141 11080 Z= 0.260 Chirality : 0.043 0.155 1264 Planarity : 0.003 0.047 1468 Dihedral : 4.861 56.983 1180 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.04 % Allowed : 9.74 % Favored : 89.21 % 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: 1.32 (0.25), residues: 1117 helix: 1.71 (0.22), residues: 535 sheet: 0.38 (0.36), residues: 185 loop : 0.09 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 221 HIS 0.004 0.001 HIS D 138 PHE 0.012 0.001 PHE C 133 TYR 0.018 0.002 TYR C 169 ARG 0.004 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7691 (tmtt) REVERT: D 92 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7791 (tmtt) outliers start: 9 outliers final: 1 residues processed: 84 average time/residue: 1.5339 time to fit residues: 136.6712 Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain D residue 92 LYS Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8168 Z= 0.270 Angle : 0.488 8.397 11080 Z= 0.265 Chirality : 0.043 0.139 1264 Planarity : 0.003 0.046 1468 Dihedral : 4.435 57.208 1176 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.16 % Allowed : 9.98 % Favored : 88.86 % 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: 1.42 (0.25), residues: 1117 helix: 1.76 (0.22), residues: 535 sheet: 0.38 (0.36), residues: 185 loop : 0.22 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 221 HIS 0.006 0.001 HIS C 138 PHE 0.011 0.002 PHE C 133 TYR 0.019 0.002 TYR C 169 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: C 186 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7215 (tt0) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 1.5447 time to fit residues: 131.9564 Evaluate side-chains 83 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8246 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8168 Z= 0.198 Angle : 0.463 7.772 11080 Z= 0.250 Chirality : 0.042 0.136 1264 Planarity : 0.003 0.046 1468 Dihedral : 3.826 18.005 1172 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.58 % Allowed : 11.37 % Favored : 88.05 % 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: 1.60 (0.26), residues: 1117 helix: 1.93 (0.22), residues: 535 sheet: 0.47 (0.37), residues: 183 loop : 0.27 (0.33), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 221 HIS 0.004 0.001 HIS A 138 PHE 0.011 0.001 PHE C 133 TYR 0.020 0.002 TYR C 169 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: C 186 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: D 226 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7372 (mtm110) outliers start: 5 outliers final: 1 residues processed: 78 average time/residue: 1.4781 time to fit residues: 121.8967 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.2980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8265 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8168 Z= 0.248 Angle : 0.479 8.151 11080 Z= 0.260 Chirality : 0.043 0.148 1264 Planarity : 0.003 0.044 1468 Dihedral : 3.878 18.910 1172 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.81 % Allowed : 11.14 % Favored : 88.05 % 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: 1.62 (0.26), residues: 1117 helix: 1.92 (0.22), residues: 535 sheet: 0.42 (0.37), residues: 185 loop : 0.37 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 221 HIS 0.005 0.001 HIS C 138 PHE 0.011 0.001 PHE C 133 TYR 0.020 0.003 TYR C 169 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7190 (tt0) REVERT: B 45 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8140 (mttt) REVERT: C 186 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7201 (tt0) outliers start: 7 outliers final: 1 residues processed: 76 average time/residue: 1.5108 time to fit residues: 121.2401 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 96 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.8255 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8168 Z= 0.222 Angle : 0.470 8.503 11080 Z= 0.254 Chirality : 0.043 0.155 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.830 19.315 1172 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.58 % Allowed : 11.25 % Favored : 88.17 % 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: 1.70 (0.26), residues: 1117 helix: 1.99 (0.22), residues: 535 sheet: 0.47 (0.37), residues: 183 loop : 0.39 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 221 HIS 0.004 0.001 HIS D 138 PHE 0.011 0.001 PHE B 133 TYR 0.020 0.003 TYR C 169 ARG 0.002 0.000 ARG C 257 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: B 45 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8187 (mttt) REVERT: C 186 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7192 (tt0) outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 1.5820 time to fit residues: 125.4084 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 10.0000 chunk 18 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 89 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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: 0.8220 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8168 Z= 0.151 Angle : 0.437 7.770 11080 Z= 0.236 Chirality : 0.042 0.145 1264 Planarity : 0.003 0.047 1468 Dihedral : 3.678 20.309 1172 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.58 % Allowed : 11.25 % Favored : 88.17 % 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: 1.86 (0.26), residues: 1117 helix: 2.14 (0.22), residues: 535 sheet: 0.46 (0.37), residues: 183 loop : 0.49 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 221 HIS 0.003 0.001 HIS B 138 PHE 0.009 0.001 PHE A 133 TYR 0.021 0.002 TYR C 169 ARG 0.004 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8162 (mttt) REVERT: C 186 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7169 (tt0) outliers start: 5 outliers final: 1 residues processed: 77 average time/residue: 1.4937 time to fit residues: 121.6235 Evaluate side-chains 79 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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: 0.8245 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8168 Z= 0.205 Angle : 0.450 7.232 11080 Z= 0.245 Chirality : 0.042 0.153 1264 Planarity : 0.003 0.046 1468 Dihedral : 3.760 23.333 1172 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.81 % Allowed : 11.14 % Favored : 88.05 % 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: 1.85 (0.26), residues: 1117 helix: 2.09 (0.22), residues: 535 sheet: 0.46 (0.37), residues: 183 loop : 0.54 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 221 HIS 0.004 0.001 HIS B 138 PHE 0.010 0.001 PHE C 133 TYR 0.020 0.002 TYR D 169 ARG 0.003 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8173 (mttt) REVERT: C 186 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7191 (tt0) outliers start: 7 outliers final: 1 residues processed: 77 average time/residue: 1.4595 time to fit residues: 118.8899 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.0370 chunk 24 optimal weight: 0.8980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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: 0.8244 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8168 Z= 0.202 Angle : 0.449 6.774 11080 Z= 0.246 Chirality : 0.042 0.155 1264 Planarity : 0.003 0.047 1468 Dihedral : 3.762 23.523 1172 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.35 % Allowed : 11.60 % Favored : 88.05 % 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: 1.86 (0.26), residues: 1117 helix: 2.08 (0.22), residues: 535 sheet: 0.46 (0.37), residues: 183 loop : 0.58 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 221 HIS 0.004 0.001 HIS C 138 PHE 0.011 0.001 PHE C 133 TYR 0.022 0.002 TYR D 169 ARG 0.003 0.000 ARG D 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8179 (mttt) REVERT: C 186 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7186 (tt0) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 1.5735 time to fit residues: 126.2682 Evaluate side-chains 78 residues out of total 784 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain D residue 161 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.099834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.072611 restraints weight = 131972.571| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 4.75 r_work: 0.2906 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8168 Z= 0.260 Angle : 0.472 8.719 11080 Z= 0.259 Chirality : 0.043 0.155 1264 Planarity : 0.003 0.045 1468 Dihedral : 3.861 23.481 1172 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.35 % Allowed : 11.48 % Favored : 88.17 % 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: 1.77 (0.26), residues: 1117 helix: 1.99 (0.22), residues: 535 sheet: 0.46 (0.37), residues: 183 loop : 0.56 (0.34), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 221 HIS 0.004 0.001 HIS C 138 PHE 0.010 0.001 PHE B 133 TYR 0.024 0.003 TYR C 169 ARG 0.003 0.000 ARG D 226 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3314.00 seconds wall clock time: 58 minutes 52.69 seconds (3532.69 seconds total)