Starting phenix.real_space_refine on Mon Apr 8 08:15:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/04_2024/8g2y_29684_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/04_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_29684/04_2024/8g2y_29684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/04_2024/8g2y_29684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/04_2024/8g2y_29684_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2y_29684/04_2024/8g2y_29684_neut_updated.pdb" } 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 Residue "A ASP 229": "OD1" <-> "OD2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B ASP 323": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 109": "OD1" <-> "OD2" Residue "R PHE 672": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13019 Number of models: 1 Model: "" Number of chains: 5 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: 3907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3907 Unusual residues: {'LPC': 1} Classifications: {'peptide': 251, 'undetermined': 1} Link IDs: {'PTRANS': 7, 'TRANS': 243, None: 1} Not linked: pdbres="LEU R 848 " pdbres="LPC R1001 " 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 Time building chain proxies: 6.33, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.51 Conformation dependent library (CDL) restraints added in 1.4 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... running ksdssp... Secondary structure from input PDB file: 20 helices and 11 sheets defined 34.3% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 26 through 39 removed outlier: 3.598A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 277 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 294 through 302 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.915A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 Processing helix chain 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 570 through 572 No H-bonds generated for 'chain 'R' and resid 570 through 572' Processing helix chain 'R' and resid 583 through 607 Processing helix chain 'R' and resid 619 through 646 Processing helix chain 'R' and resid 656 through 687 removed outlier: 3.572A pdb=" N PHE R 662 " --> pdb=" O THR R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 695 through 721 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 741 through 769 Proline residue: R 750 - end of helix Processing helix chain 'R' and resid 786 through 800 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 811 Processing helix chain 'R' and resid 818 through 837 removed outlier: 5.993A pdb=" N GLY R 831 " --> pdb=" O ASN R 827 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N PHE R 832 " --> pdb=" O ALA R 828 " (cutoff:3.500A) Processing helix chain 'R' and resid 843 through 847 Processing sheet with id= A, first strand: chain 'A' and resid 44 through 46 Processing sheet with id= B, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.719A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing sheet with id= C, 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= D, first strand: chain 'B' and resid 111 through 114 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= E, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.869A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 208 through 212 removed outlier: 3.782A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 240 through 243 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= H, first strand: chain 'B' and resid 295 through 298 Processing sheet with id= I, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.508A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 18 through 23 Processing sheet with id= K, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.808A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 305 hydrogen bonds defined for protein. 858 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: 4.66 Time building geometry restraints manager: 10.87 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: 92.83 - 101.15: 8 101.15 - 109.47: 8526 109.47 - 117.79: 8589 117.79 - 126.11: 6308 126.11 - 134.43: 169 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: 1392 2.25 - 2.83: 27928 2.83 - 3.42: 33242 3.42 - 4.01: 45176 4.01 - 4.60: 69366 Nonbonded interactions: 177104 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 1.850 nonbonded pdb=" O GLU B 226 " pdb="HH12 ARG N 98 " model vdw 1.730 1.850 nonbonded pdb=" O LEU A 291 " pdb="HE21 GLN A 294 " model vdw 1.732 1.850 nonbonded pdb=" OE2 GLU A 344 " pdb="HH21 ARG A 347 " model vdw 1.747 1.850 ... (remaining 177099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.210 Extract box with map and model: 7.360 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 43.870 Find NCS groups from input model: 0.220 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.500 ------------------------------------------------------------------------------- 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= 0.297 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.977 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: 0.4071 time to fit residues: 66.7281 Evaluate side-chains 110 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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: 3.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6822 Z= 0.240 Angle : 0.495 5.842 9292 Z= 0.265 Chirality : 0.039 0.142 1104 Planarity : 0.004 0.061 1142 Dihedral : 6.327 55.596 963 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.29 % Allowed : 19.11 % Favored : 78.59 % 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: 1.31 (0.30), residues: 321 sheet: -2.65 (0.32), residues: 211 loop : -1.35 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 0.002 0.000 ARG R 624 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7575 (mp) REVERT: R 721 THR cc_start: 0.5846 (t) cc_final: 0.5572 (t) outliers start: 15 outliers final: 10 residues processed: 113 average time/residue: 0.3858 time to fit residues: 59.5226 Evaluate side-chains 112 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 657 CYS Chi-restraints excluded: chain R residue 735 LEU Chi-restraints excluded: chain R residue 745 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.1109 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= 0.252 Angle : 0.491 5.843 9292 Z= 0.267 Chirality : 0.039 0.149 1104 Planarity : 0.004 0.061 1142 Dihedral : 5.622 55.929 963 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.52 % Allowed : 18.96 % 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: -1.08 (0.30), residues: 861 helix: 1.43 (0.30), residues: 321 sheet: -2.66 (0.32), residues: 211 loop : -1.41 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.003 0.001 HIS B 91 PHE 0.009 0.001 PHE R 837 TYR 0.008 0.001 TYR R 684 ARG 0.002 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8190 (p) REVERT: R 721 THR cc_start: 0.5815 (t) cc_final: 0.5522 (t) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.3512 time to fit residues: 58.6101 Evaluate side-chains 117 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 97 SER 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 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 N residue 114 THR Chi-restraints excluded: chain N residue 122 THR 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 735 LEU Chi-restraints excluded: chain R residue 745 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6822 Z= 0.151 Angle : 0.448 5.617 9292 Z= 0.240 Chirality : 0.038 0.141 1104 Planarity : 0.003 0.061 1142 Dihedral : 5.343 57.320 963 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.29 % Allowed : 18.96 % 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: -0.88 (0.30), residues: 861 helix: 1.61 (0.30), residues: 320 sheet: -2.60 (0.33), residues: 211 loop : -1.29 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.000 HIS B 91 PHE 0.007 0.001 PHE B 199 TYR 0.006 0.001 TYR B 289 ARG 0.001 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 684 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7401 (t80) REVERT: R 721 THR cc_start: 0.5697 (t) cc_final: 0.5401 (t) outliers start: 15 outliers final: 12 residues processed: 114 average time/residue: 0.3749 time to fit residues: 58.2628 Evaluate side-chains 117 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 126 VAL 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 745 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: 2.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1353 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= 0.244 Angle : 0.478 5.723 9292 Z= 0.260 Chirality : 0.039 0.143 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.501 57.128 963 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 4.43 % Allowed : 17.58 % Favored : 77.98 % 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: -0.95 (0.30), residues: 861 helix: 1.60 (0.30), residues: 320 sheet: -2.64 (0.33), residues: 205 loop : -1.41 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE R 747 TYR 0.007 0.001 TYR N 115 ARG 0.001 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 627 MET cc_start: 0.8336 (mmm) cc_final: 0.8042 (mmm) REVERT: R 684 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7440 (t80) REVERT: R 721 THR cc_start: 0.5688 (t) cc_final: 0.5398 (t) outliers start: 29 outliers final: 22 residues processed: 125 average time/residue: 0.3598 time to fit residues: 61.9960 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 122 SER 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 228 ASP 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 B residue 339 TRP Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL 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 745 LEU Chi-restraints excluded: chain R residue 797 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.0010 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- 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: 0.7640 moved from start: 0.1456 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= 0.248 Angle : 0.484 5.672 9292 Z= 0.263 Chirality : 0.039 0.143 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.589 57.755 963 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.59 % Allowed : 17.89 % 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: -1.04 (0.30), residues: 861 helix: 1.58 (0.30), residues: 320 sheet: -2.75 (0.32), residues: 205 loop : -1.47 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS B 91 PHE 0.012 0.001 PHE R 837 TYR 0.008 0.001 TYR N 115 ARG 0.001 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 106 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8530 (OUTLIER) cc_final: 0.8192 (p) REVERT: N 109 ASP cc_start: 0.8543 (m-30) cc_final: 0.8094 (m-30) REVERT: R 684 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7444 (t80) REVERT: R 721 THR cc_start: 0.5649 (t) cc_final: 0.5344 (t) outliers start: 30 outliers final: 22 residues processed: 127 average time/residue: 0.3636 time to fit residues: 64.3371 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 292 PHE 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 N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL 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 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: 1.9990 chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6822 Z= 0.320 Angle : 0.520 5.451 9292 Z= 0.284 Chirality : 0.040 0.158 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.716 57.696 963 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 5.05 % Allowed : 17.58 % Favored : 77.37 % 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: -1.30 (0.30), residues: 861 helix: 1.42 (0.30), residues: 320 sheet: -2.90 (0.30), residues: 223 loop : -1.56 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.002 PHE B 199 TYR 0.008 0.001 TYR N 115 ARG 0.002 0.000 ARG R 624 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8542 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 318 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8461 (tt) REVERT: R 627 MET cc_start: 0.8241 (mmm) cc_final: 0.7925 (mmm) REVERT: R 684 TYR cc_start: 0.8025 (OUTLIER) cc_final: 0.7518 (t80) REVERT: R 721 THR cc_start: 0.5707 (t) cc_final: 0.5408 (t) outliers start: 33 outliers final: 25 residues processed: 128 average time/residue: 0.3910 time to fit residues: 68.0034 Evaluate side-chains 130 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU 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 114 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL 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 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: 0.8980 chunk 7 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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: 0.7659 moved from start: 0.1693 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= 0.255 Angle : 0.494 5.375 9292 Z= 0.269 Chirality : 0.039 0.143 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.609 58.167 963 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 4.59 % Allowed : 18.35 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.30), residues: 861 helix: 1.45 (0.30), residues: 321 sheet: -2.91 (0.31), residues: 219 loop : -1.58 (0.34), residues: 321 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 B 199 TYR 0.009 0.001 TYR N 115 ARG 0.009 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 100 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.8152 (p) REVERT: B 318 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8467 (tt) REVERT: R 627 MET cc_start: 0.8237 (mmm) cc_final: 0.7924 (mmm) REVERT: R 684 TYR cc_start: 0.7992 (OUTLIER) cc_final: 0.7516 (t80) REVERT: R 721 THR cc_start: 0.5720 (t) cc_final: 0.5421 (t) outliers start: 30 outliers final: 25 residues processed: 122 average time/residue: 0.3841 time to fit residues: 63.8276 Evaluate side-chains 127 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 163 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU 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 114 THR Chi-restraints excluded: chain N residue 126 VAL 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 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: 1.9990 chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.7662 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6822 Z= 0.258 Angle : 0.493 5.428 9292 Z= 0.268 Chirality : 0.039 0.144 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.584 58.998 963 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.74 % Allowed : 18.35 % 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: -1.30 (0.30), residues: 861 helix: 1.44 (0.30), residues: 321 sheet: -2.93 (0.31), residues: 218 loop : -1.60 (0.34), residues: 322 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 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR N 115 ARG 0.006 0.000 ARG R 685 *********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8212 (p) REVERT: B 318 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (tt) REVERT: R 627 MET cc_start: 0.8234 (mmm) cc_final: 0.7898 (mmm) REVERT: R 684 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.7492 (t80) REVERT: R 721 THR cc_start: 0.5769 (t) cc_final: 0.5476 (t) outliers start: 31 outliers final: 24 residues processed: 125 average time/residue: 0.3746 time to fit residues: 63.9089 Evaluate side-chains 130 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU 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 114 THR Chi-restraints excluded: chain N residue 126 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.7641 moved from start: 0.1749 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= 0.201 Angle : 0.470 5.327 9292 Z= 0.254 Chirality : 0.039 0.141 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.450 58.977 963 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 4.13 % Allowed : 19.11 % 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: -1.19 (0.30), residues: 861 helix: 1.52 (0.30), residues: 321 sheet: -2.84 (0.31), residues: 219 loop : -1.55 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.001 HIS B 142 PHE 0.009 0.001 PHE B 199 TYR 0.008 0.001 TYR N 115 ARG 0.006 0.000 ARG R 685 ********************** 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. Residue LEU 848 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8190 (p) REVERT: B 318 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8503 (tt) REVERT: R 627 MET cc_start: 0.8201 (mmm) cc_final: 0.7911 (mmm) REVERT: R 684 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7444 (t80) REVERT: R 721 THR cc_start: 0.5653 (t) cc_final: 0.5354 (t) outliers start: 27 outliers final: 22 residues processed: 125 average time/residue: 0.3747 time to fit residues: 63.8715 Evaluate side-chains 128 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 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 218 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU 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 114 THR Chi-restraints excluded: chain N residue 126 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 0.0010 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.159322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124281 restraints weight = 21945.943| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.37 r_work: 0.3257 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1766 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= 0.213 Angle : 0.480 5.399 9292 Z= 0.260 Chirality : 0.039 0.142 1104 Planarity : 0.004 0.059 1142 Dihedral : 5.424 59.507 963 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.43 % Allowed : 18.81 % 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: -1.20 (0.30), residues: 861 helix: 1.56 (0.30), residues: 320 sheet: -2.88 (0.31), residues: 218 loop : -1.58 (0.34), residues: 323 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 0.010 0.001 PHE B 199 TYR 0.008 0.001 TYR N 115 ARG 0.006 0.000 ARG R 685 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3598.30 seconds wall clock time: 64 minutes 55.28 seconds (3895.28 seconds total)