Starting phenix.real_space_refine on Sun Nov 17 06:51:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/11_2024/8g2y_29684_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 45 5.16 5 C 4340 2.51 5 N 1123 2.21 5 O 1168 1.98 5 H 6342 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13019 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2951 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 189} Chain breaks: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 4062 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 286} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 452 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "N" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1647 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "R" Number of atoms: 3876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 3876 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 4 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 43 Chain: "R" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LPC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.85, per 1000 atoms: 0.53 Number of scatterers: 13019 At special positions: 0 Unit cell: (75.075, 86.625, 119.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 P 1 15.00 O 1168 8.00 N 1123 7.00 C 4340 6.00 H 6342 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 657 " - pdb=" SG CYS R 733 " distance=2.03 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: 3.35 Conformation dependent library (CDL) restraints added in 1.2 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1666 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 37.9% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 removed outlier: 3.621A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 278 removed outlier: 4.044A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.510A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.915A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.809A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.540A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 569 through 573 Processing helix chain 'R' and resid 582 through 608 Processing helix chain 'R' and resid 619 through 647 removed outlier: 3.607A pdb=" N VAL R 647 " --> pdb=" O VAL R 643 " (cutoff:3.500A) Processing helix chain 'R' and resid 656 through 688 removed outlier: 3.572A pdb=" N PHE R 662 " --> pdb=" O THR R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 694 through 722 removed outlier: 4.822A pdb=" N CYS R 709 " --> pdb=" O LEU R 705 " (cutoff:3.500A) Proline residue: R 710 - end of helix Processing helix chain 'R' and resid 740 through 770 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 786 through 801 removed outlier: 3.894A pdb=" N GLY R 790 " --> pdb=" O ILE R 786 " (cutoff:3.500A) Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 805 Processing helix chain 'R' and resid 806 through 811 removed outlier: 3.706A pdb=" N THR R 810 " --> pdb=" O PHE R 806 " (cutoff:3.500A) Processing helix chain 'R' and resid 817 through 829 Processing helix chain 'R' and resid 829 through 838 Processing helix chain 'R' and resid 842 through 848 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.724A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 6.196A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.138A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.007A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 93 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.893A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.671A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.782A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.837A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.245A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.612A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 924 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: 4.92 Time building geometry restraints manager: 3.96 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: 6308 1.03 - 1.23: 47 1.23 - 1.42: 2885 1.42 - 1.62: 3861 1.62 - 1.81: 63 Bond restraints: 13164 Sorted by residual: bond pdb=" N ARG N 57 " pdb=" H ARG N 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N LEU A 272 " pdb=" H LEU A 272 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" CG LEU A 272 " pdb=" HG LEU A 272 " ideal model delta sigma weight residual 0.970 1.111 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" CB LEU A 272 " pdb=" HB3 LEU A 272 " ideal model delta sigma weight residual 0.970 1.108 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CB LEU A 272 " pdb=" HB2 LEU A 272 " ideal model delta sigma weight residual 0.970 1.108 -0.138 2.00e-02 2.50e+03 4.77e+01 ... (remaining 13159 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 22901 1.80 - 3.60: 599 3.60 - 5.40: 84 5.40 - 7.19: 12 7.19 - 8.99: 4 Bond angle restraints: 23600 Sorted by residual: angle pdb=" CA VAL N 48 " pdb=" C VAL N 48 " pdb=" O VAL N 48 " ideal model delta sigma weight residual 120.32 114.09 6.23 1.10e+00 8.26e-01 3.21e+01 angle pdb=" CA TRP N 47 " pdb=" C TRP N 47 " pdb=" O TRP N 47 " ideal model delta sigma weight residual 120.54 115.32 5.22 1.13e+00 7.83e-01 2.13e+01 angle pdb=" C VAL N 48 " pdb=" CA VAL N 48 " pdb=" CB VAL N 48 " ideal model delta sigma weight residual 111.55 106.67 4.88 1.15e+00 7.56e-01 1.80e+01 angle pdb=" N ASP B 170 " pdb=" CA ASP B 170 " pdb=" C ASP B 170 " ideal model delta sigma weight residual 109.50 102.86 6.64 1.58e+00 4.01e-01 1.77e+01 angle pdb=" CA THR N 61 " pdb=" C THR N 61 " pdb=" O THR N 61 " ideal model delta sigma weight residual 122.03 117.31 4.72 1.13e+00 7.83e-01 1.74e+01 ... (remaining 23595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5457 16.81 - 33.61: 573 33.61 - 50.42: 167 50.42 - 67.22: 69 67.22 - 84.03: 13 Dihedral angle restraints: 6279 sinusoidal: 3157 harmonic: 3122 Sorted by residual: dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLY R 838 " pdb=" C GLY R 838 " pdb=" N ILE R 839 " pdb=" CA ILE R 839 " ideal model delta harmonic sigma weight residual -180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" C THR N 61 " pdb=" N THR N 61 " pdb=" CA THR N 61 " pdb=" CB THR N 61 " ideal model delta harmonic sigma weight residual -122.00 -112.69 -9.31 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 6276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 702 0.036 - 0.071: 289 0.071 - 0.107: 72 0.107 - 0.142: 35 0.142 - 0.178: 6 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" CB VAL N 48 " pdb=" CA VAL N 48 " pdb=" CG1 VAL N 48 " pdb=" CG2 VAL N 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 1101 not shown) Planarity restraints: 1996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN R 816 " -0.248 2.00e-02 2.50e+03 3.67e-01 2.02e+03 pdb=" CG ASN R 816 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN R 816 " 0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN R 816 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 816 " -0.593 2.00e-02 2.50e+03 pdb="HD22 ASN R 816 " 0.581 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL N 48 " 0.025 2.00e-02 2.50e+03 4.79e-02 2.30e+01 pdb=" N SER N 49 " -0.083 2.00e-02 2.50e+03 pdb=" CA SER N 49 " 0.022 2.00e-02 2.50e+03 pdb=" H SER N 49 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 84 " 0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" N TYR B 85 " -0.067 2.00e-02 2.50e+03 pdb=" CA TYR B 85 " 0.017 2.00e-02 2.50e+03 pdb=" H TYR B 85 " 0.029 2.00e-02 2.50e+03 ... (remaining 1993 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 1394 2.25 - 2.83: 27900 2.83 - 3.42: 33224 3.42 - 4.01: 45162 4.01 - 4.60: 69319 Nonbonded interactions: 176999 Sorted by model distance: nonbonded pdb="HH21 ARG A 231 " pdb="HD21 LEU A 272 " model vdw 1.657 2.270 nonbonded pdb=" O GLY R 809 " pdb=" H ASP R 813 " model vdw 1.722 2.450 nonbonded pdb=" O GLU B 226 " pdb="HH12 ARG N 98 " model vdw 1.730 2.450 nonbonded pdb=" O LEU A 291 " pdb="HE21 GLN A 294 " model vdw 1.732 2.450 nonbonded pdb=" OE2 GLU A 344 " pdb="HH21 ARG A 347 " model vdw 1.747 2.450 ... (remaining 176994 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.250 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 30.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.051 6822 Z= 0.283 Angle : 0.763 8.993 9292 Z= 0.432 Chirality : 0.045 0.178 1104 Planarity : 0.005 0.073 1142 Dihedral : 15.564 84.025 2252 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 20.80 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.29), residues: 861 helix: 0.72 (0.30), residues: 320 sheet: -2.52 (0.32), residues: 211 loop : -1.35 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 47 HIS 0.003 0.001 HIS R 665 PHE 0.014 0.001 PHE R 672 TYR 0.009 0.001 TYR R 684 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 TRP cc_start: 0.7661 (m100) cc_final: 0.7420 (m100) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4091 time to fit residues: 67.0105 Evaluate side-chains 110 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.2980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6822 Z= 0.166 Angle : 0.488 5.799 9292 Z= 0.261 Chirality : 0.039 0.141 1104 Planarity : 0.004 0.061 1142 Dihedral : 6.289 56.515 963 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.38 % Allowed : 19.72 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.29), residues: 861 helix: 1.33 (0.30), residues: 326 sheet: -2.53 (0.32), residues: 208 loop : -1.54 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.005 0.001 HIS A 41 PHE 0.010 0.001 PHE R 747 TYR 0.010 0.001 TYR B 105 ARG 0.002 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7531 (mp) REVERT: R 721 THR cc_start: 0.5899 (t) cc_final: 0.5610 (t) outliers start: 9 outliers final: 5 residues processed: 112 average time/residue: 0.3856 time to fit residues: 59.1890 Evaluate side-chains 112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6822 Z= 0.212 Angle : 0.482 5.861 9292 Z= 0.261 Chirality : 0.039 0.147 1104 Planarity : 0.004 0.060 1142 Dihedral : 5.525 55.429 963 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.14 % Allowed : 19.72 % Favored : 78.13 % 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: -1.02 (0.29), residues: 861 helix: 1.52 (0.30), residues: 327 sheet: -2.58 (0.32), residues: 208 loop : -1.55 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE R 747 TYR 0.010 0.001 TYR R 684 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 721 THR cc_start: 0.5775 (t) cc_final: 0.5488 (t) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.3765 time to fit residues: 61.9625 Evaluate side-chains 120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6822 Z= 0.132 Angle : 0.443 5.550 9292 Z= 0.240 Chirality : 0.038 0.138 1104 Planarity : 0.003 0.058 1142 Dihedral : 5.301 56.783 963 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.99 % Allowed : 19.27 % Favored : 78.75 % 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: -0.86 (0.29), residues: 861 helix: 1.67 (0.30), residues: 327 sheet: -2.51 (0.33), residues: 208 loop : -1.48 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.000 HIS B 91 PHE 0.007 0.001 PHE R 747 TYR 0.008 0.001 TYR N 60 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 721 THR cc_start: 0.5786 (t) cc_final: 0.5516 (t) outliers start: 13 outliers final: 11 residues processed: 117 average time/residue: 0.3725 time to fit residues: 59.8572 Evaluate side-chains 119 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.7620 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6822 Z= 0.249 Angle : 0.491 5.518 9292 Z= 0.267 Chirality : 0.039 0.148 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.479 56.823 963 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.75 % Allowed : 19.72 % Favored : 77.52 % 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: -0.98 (0.29), residues: 861 helix: 1.62 (0.30), residues: 327 sheet: -2.64 (0.32), residues: 208 loop : -1.54 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.010 0.001 PHE R 747 TYR 0.009 0.001 TYR R 684 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 684 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7446 (t80) REVERT: R 721 THR cc_start: 0.5780 (t) cc_final: 0.5510 (t) outliers start: 18 outliers final: 15 residues processed: 120 average time/residue: 0.3870 time to fit residues: 64.5915 Evaluate side-chains 121 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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: 0.7619 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6822 Z= 0.223 Angle : 0.480 5.477 9292 Z= 0.261 Chirality : 0.039 0.143 1104 Planarity : 0.003 0.057 1142 Dihedral : 5.519 56.794 963 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.91 % Allowed : 20.18 % Favored : 76.91 % 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: -0.97 (0.30), residues: 861 helix: 1.65 (0.30), residues: 328 sheet: -2.66 (0.33), residues: 208 loop : -1.55 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE R 747 TYR 0.008 0.001 TYR N 95 ARG 0.003 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 684 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7461 (t80) REVERT: R 721 THR cc_start: 0.5800 (t) cc_final: 0.5538 (t) outliers start: 19 outliers final: 17 residues processed: 123 average time/residue: 0.3449 time to fit residues: 58.8111 Evaluate side-chains 127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6822 Z= 0.238 Angle : 0.488 5.339 9292 Z= 0.266 Chirality : 0.039 0.144 1104 Planarity : 0.003 0.056 1142 Dihedral : 5.539 56.827 963 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.67 % Allowed : 19.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.30), residues: 861 helix: 1.65 (0.30), residues: 327 sheet: -2.68 (0.33), residues: 208 loop : -1.60 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.009 0.001 PHE R 747 TYR 0.008 0.001 TYR N 60 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 684 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.7457 (t80) REVERT: R 721 THR cc_start: 0.5797 (t) cc_final: 0.5539 (t) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.3487 time to fit residues: 60.0104 Evaluate side-chains 125 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.7661 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6822 Z= 0.314 Angle : 0.527 5.388 9292 Z= 0.289 Chirality : 0.040 0.149 1104 Planarity : 0.004 0.056 1142 Dihedral : 5.698 57.987 963 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.28 % Allowed : 18.50 % Favored : 77.22 % 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: -1.16 (0.29), residues: 861 helix: 1.50 (0.30), residues: 328 sheet: -2.76 (0.32), residues: 214 loop : -1.64 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.010 0.001 PHE R 747 TYR 0.010 0.001 TYR R 707 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 ARG cc_start: 0.8126 (ptp-170) cc_final: 0.7753 (ptp-170) REVERT: B 97 SER cc_start: 0.8673 (OUTLIER) cc_final: 0.8470 (p) REVERT: R 684 TYR cc_start: 0.8002 (OUTLIER) cc_final: 0.7502 (t80) REVERT: R 721 THR cc_start: 0.5793 (t) cc_final: 0.5527 (t) outliers start: 28 outliers final: 22 residues processed: 130 average time/residue: 0.3609 time to fit residues: 65.1306 Evaluate side-chains 131 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 797 THR Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.7666 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6822 Z= 0.309 Angle : 0.531 5.185 9292 Z= 0.292 Chirality : 0.040 0.150 1104 Planarity : 0.004 0.056 1142 Dihedral : 5.738 58.850 963 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.67 % Allowed : 19.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.29), residues: 861 helix: 1.39 (0.30), residues: 328 sheet: -2.81 (0.32), residues: 209 loop : -1.71 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 819 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE R 747 TYR 0.009 0.001 TYR N 115 ARG 0.003 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8432 (p) REVERT: R 684 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7487 (t80) REVERT: R 721 THR cc_start: 0.5812 (t) cc_final: 0.5552 (t) outliers start: 24 outliers final: 21 residues processed: 126 average time/residue: 0.3771 time to fit residues: 65.4389 Evaluate side-chains 130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 568 SER Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7628 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6822 Z= 0.193 Angle : 0.487 5.072 9292 Z= 0.265 Chirality : 0.039 0.145 1104 Planarity : 0.004 0.057 1142 Dihedral : 5.503 59.050 963 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.21 % Allowed : 20.03 % Favored : 76.76 % 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: -1.11 (0.30), residues: 861 helix: 1.56 (0.30), residues: 327 sheet: -2.80 (0.31), residues: 219 loop : -1.53 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE R 837 TYR 0.008 0.001 TYR N 115 ARG 0.003 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LYS 211 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue THR 369 is missing expected H atoms. Skipping. Residue MET 45 is missing expected H atoms. Skipping. Residue SER 84 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue THR 196 is missing expected H atoms. Skipping. Residue MET 217 is missing expected H atoms. Skipping. Residue MET 262 is missing expected H atoms. Skipping. Residue SER 265 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue SER 331 is missing expected H atoms. Skipping. Residue SER 334 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 69 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 85 is missing expected H atoms. Skipping. Residue THR 91 is missing expected H atoms. Skipping. Residue THR 125 is missing expected H atoms. Skipping. Residue SER 579 is missing expected H atoms. Skipping. Residue THR 580 is missing expected H atoms. Skipping. Residue VAL 584 is missing expected H atoms. Skipping. Residue LYS 586 is missing expected H atoms. Skipping. Residue MET 693 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue SER 741 is missing expected H atoms. Skipping. Residue THR 785 is missing expected H atoms. Skipping. Residue SER 814 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 684 TYR cc_start: 0.7949 (OUTLIER) cc_final: 0.7457 (t80) REVERT: R 721 THR cc_start: 0.5782 (t) cc_final: 0.5509 (t) outliers start: 21 outliers final: 19 residues processed: 128 average time/residue: 0.3826 time to fit residues: 66.1643 Evaluate side-chains 129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 642 ILE Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 684 TYR Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 836 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 60 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.159396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.123937 restraints weight = 21893.178| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.36 r_work: 0.3249 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6822 Z= 0.238 Angle : 0.512 5.161 9292 Z= 0.278 Chirality : 0.040 0.145 1104 Planarity : 0.004 0.056 1142 Dihedral : 5.554 59.597 963 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.52 % Allowed : 19.72 % Favored : 76.76 % 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: -1.17 (0.30), residues: 861 helix: 1.49 (0.30), residues: 328 sheet: -2.82 (0.31), residues: 219 loop : -1.55 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.017 0.001 PHE R 837 TYR 0.008 0.001 TYR R 684 ARG 0.008 0.000 ARG R 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3588.26 seconds wall clock time: 64 minutes 42.75 seconds (3882.75 seconds total)