Starting phenix.real_space_refine on Wed Feb 14 11:31:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tyi_20583/02_2024/6tyi_20583_updated.pdb" } resolution = 3.3 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= 0.008 sd= 0.148 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 36 5.16 5 C 5894 2.51 5 N 1567 2.21 5 O 1683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A ARG 66": "NH1" <-> "NH2" Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 105": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C ARG 117": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E GLU 227": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9184 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1702 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 221} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1704 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 4, 'TRANS': 220} Chain: "C" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1712 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 4, 'TRANS': 221} Chain: "E" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1696 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain: "Y" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 236 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 224 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.60 Number of scatterers: 9184 At special positions: 0 Unit cell: (84.8, 84.8, 121.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 4 15.00 O 1683 8.00 N 1567 7.00 C 5894 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.7 seconds 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 0 sheets defined 81.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 22 through 62 removed outlier: 4.514A pdb=" N VAL A 46 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 76 Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 104 through 127 Processing helix chain 'A' and resid 130 through 158 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 171 through 174 No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 177 through 232 Proline residue: A 190 - end of helix Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 21 through 64 removed outlier: 5.182A pdb=" N GLU B 64 " --> pdb=" O GLN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 77 removed outlier: 5.423A pdb=" N ASP B 77 " --> pdb=" O ASP B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 97 removed outlier: 4.075A pdb=" N LEU B 88 " --> pdb=" O SER B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 126 Processing helix chain 'B' and resid 130 through 161 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 171 through 232 removed outlier: 3.754A pdb=" N THR B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) Proline residue: B 190 - end of helix Processing helix chain 'C' and resid 21 through 64 removed outlier: 4.454A pdb=" N GLU C 64 " --> pdb=" O GLN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 5.382A pdb=" N ASP C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 97 Processing helix chain 'C' and resid 104 through 126 Processing helix chain 'C' and resid 129 through 162 removed outlier: 3.512A pdb=" N ILE C 136 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 139 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N SER C 140 " --> pdb=" O GLY C 137 " (cutoff:3.500A) Proline residue: C 141 - end of helix removed outlier: 3.536A pdb=" N VAL C 149 " --> pdb=" O PHE C 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 162 " --> pdb=" O ILE C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 231 Proline residue: C 190 - end of helix Processing helix chain 'D' and resid 12 through 15 No H-bonds generated for 'chain 'D' and resid 12 through 15' Processing helix chain 'D' and resid 22 through 64 removed outlier: 4.909A pdb=" N GLU D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 104 through 127 Processing helix chain 'D' and resid 130 through 160 Proline residue: D 141 - end of helix Processing helix chain 'D' and resid 171 through 232 removed outlier: 3.666A pdb=" N ALA D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR D 181 " --> pdb=" O ALA D 177 " (cutoff:3.500A) Proline residue: D 190 - end of helix Processing helix chain 'E' and resid 24 through 64 removed outlier: 4.278A pdb=" N GLY E 29 " --> pdb=" O CYS E 25 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 77 removed outlier: 5.054A pdb=" N ASP E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 97 Processing helix chain 'E' and resid 104 through 126 Processing helix chain 'E' and resid 130 through 161 Proline residue: E 141 - end of helix removed outlier: 3.813A pdb=" N ALA E 160 " --> pdb=" O PHE E 156 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 232 removed outlier: 4.184A pdb=" N ILE E 189 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Proline residue: E 190 - end of helix removed outlier: 3.622A pdb=" N ILE E 194 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 36 removed outlier: 3.962A pdb=" N VAL Y 26 " --> pdb=" O PRO Y 22 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N MET Y 27 " --> pdb=" O PHE Y 23 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL Y 29 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU Y 31 " --> pdb=" O MET Y 27 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE Y 34 " --> pdb=" O LEU Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Z' and resid 24 through 38 removed outlier: 3.611A pdb=" N ILE Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL Z 36 " --> pdb=" O ILE Z 32 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA Z 38 " --> pdb=" O PHE Z 34 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2049 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1524 1.30 - 1.43: 2284 1.43 - 1.55: 5412 1.55 - 1.68: 30 1.68 - 1.80: 67 Bond restraints: 9317 Sorted by residual: bond pdb=" C11 PGT A 301 " pdb=" O3 PGT A 301 " ideal model delta sigma weight residual 1.327 1.431 -0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C31 PGT A 301 " pdb=" O2 PGT A 301 " ideal model delta sigma weight residual 1.331 1.404 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 PEV C 301 " pdb=" O2 PEV C 301 " ideal model delta sigma weight residual 1.330 1.403 -0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C31 PEV E 301 " pdb=" O2 PEV E 301 " ideal model delta sigma weight residual 1.330 1.402 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C11 PEV C 301 " pdb=" O3 PEV C 301 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.83e+00 ... (remaining 9312 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.91: 118 105.91 - 112.95: 5301 112.95 - 119.99: 3453 119.99 - 127.02: 3627 127.02 - 134.06: 71 Bond angle restraints: 12570 Sorted by residual: angle pdb=" O3P PGT A 301 " pdb=" P PGT A 301 " pdb=" O4P PGT A 301 " ideal model delta sigma weight residual 92.82 111.48 -18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" O1P PEV C 301 " pdb=" P PEV C 301 " pdb=" O2P PEV C 301 " ideal model delta sigma weight residual 119.37 100.88 18.49 3.00e+00 1.11e-01 3.80e+01 angle pdb=" O3P PEV C 301 " pdb=" P PEV C 301 " pdb=" O4P PEV C 301 " ideal model delta sigma weight residual 93.57 111.90 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" O1P PGT A 301 " pdb=" P PGT A 301 " pdb=" O2P PGT A 301 " ideal model delta sigma weight residual 119.10 100.80 18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" O3P PEV E 301 " pdb=" P PEV E 301 " pdb=" O4P PEV E 301 " ideal model delta sigma weight residual 93.57 111.77 -18.20 3.00e+00 1.11e-01 3.68e+01 ... (remaining 12565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 5232 25.60 - 51.19: 322 51.19 - 76.79: 49 76.79 - 102.39: 6 102.39 - 127.98: 2 Dihedral angle restraints: 5611 sinusoidal: 2239 harmonic: 3372 Sorted by residual: dihedral pdb=" CA ALA A 19 " pdb=" C ALA A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 -157.81 -22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" C3 PEV C 301 " pdb=" C1 PEV C 301 " pdb=" C2 PEV C 301 " pdb=" O3P PEV C 301 " ideal model delta sinusoidal sigma weight residual 292.80 164.82 127.98 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C3 PEV B 301 " pdb=" C1 PEV B 301 " pdb=" C2 PEV B 301 " pdb=" O3P PEV B 301 " ideal model delta sinusoidal sigma weight residual 292.80 172.73 120.07 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 968 0.046 - 0.092: 424 0.092 - 0.138: 60 0.138 - 0.184: 10 0.184 - 0.230: 3 Chirality restraints: 1465 Sorted by residual: chirality pdb=" C5 PGT A 301 " pdb=" C4 PGT A 301 " pdb=" C6 PGT A 301 " pdb=" O5 PGT A 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.53 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PGT A 301 " pdb=" C1 PGT A 301 " pdb=" C3 PGT A 301 " pdb=" O2 PGT A 301 " both_signs ideal model delta sigma weight residual False 2.35 2.55 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL B 197 " pdb=" CA VAL B 197 " pdb=" CG1 VAL B 197 " pdb=" CG2 VAL B 197 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1462 not shown) Planarity restraints: 1598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " 0.017 2.00e-02 2.50e+03 1.73e-02 5.26e+00 pdb=" CG PHE A 113 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 140 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 141 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 141 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 141 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 171 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO E 172 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 172 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 172 " -0.022 5.00e-02 4.00e+02 ... (remaining 1595 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 21 2.42 - 3.04: 6144 3.04 - 3.66: 13120 3.66 - 4.28: 19520 4.28 - 4.90: 32974 Nonbonded interactions: 71779 Sorted by model distance: nonbonded pdb=" OG SER D 98 " pdb=" NH1 ARG D 110 " model vdw 1.796 2.520 nonbonded pdb=" OG SER A 98 " pdb=" NH1 ARG A 110 " model vdw 2.179 2.520 nonbonded pdb=" OE2 GLU A 58 " pdb=" OG SER A 82 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR A 148 " pdb=" O ALA A 177 " model vdw 2.237 2.440 nonbonded pdb=" OE2 GLU B 58 " pdb=" OG SER B 82 " model vdw 2.241 2.440 ... (remaining 71774 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 233) selection = (chain 'B' and resid 11 through 233) selection = (chain 'C' and resid 11 through 233) selection = (chain 'D' and resid 11 through 233) selection = (chain 'E' and resid 11 through 233) } ncs_group { reference = (chain 'Y' and resid 12 through 40) selection = chain 'Z' } 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: 0.350 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: 0.020 Extract box with map and model: 1.930 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 28.440 Find NCS groups from input model: 0.740 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 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 : 0.012 0.104 9317 Z= 0.758 Angle : 1.033 18.665 12570 Z= 0.504 Chirality : 0.049 0.230 1465 Planarity : 0.004 0.039 1598 Dihedral : 16.668 127.984 3433 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.14 % Rotamer: Outliers : 0.43 % Allowed : 10.99 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1172 helix: 0.18 (0.15), residues: 996 sheet: None (None), residues: 0 loop : -4.46 (0.30), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 38 HIS 0.009 0.001 HIS Z 16 PHE 0.040 0.003 PHE A 113 TYR 0.016 0.002 TYR D 132 ARG 0.009 0.001 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 1.023 Fit side-chains REVERT: A 94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8202 (tp30) REVERT: B 126 MET cc_start: 0.8051 (mmm) cc_final: 0.7533 (mmt) REVERT: C 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7699 (tm-30) REVERT: C 94 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5213 (mm-30) REVERT: D 128 ARG cc_start: 0.7770 (ttm170) cc_final: 0.7521 (ttp-110) REVERT: E 226 LEU cc_start: 0.8851 (mt) cc_final: 0.8548 (mp) outliers start: 4 outliers final: 3 residues processed: 152 average time/residue: 0.2905 time to fit residues: 56.4823 Evaluate side-chains 126 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain E residue 186 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 104 ASN B 70 GLN B 93 ASN C 215 GLN D 93 ASN D 125 GLN D 163 GLN D 196 ASN E 69 ASN E 93 ASN E 154 ASN E 161 GLN E 196 ASN Z 16 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9317 Z= 0.197 Angle : 0.517 6.806 12570 Z= 0.274 Chirality : 0.035 0.119 1465 Planarity : 0.005 0.030 1598 Dihedral : 12.040 126.811 1440 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.40 % Allowed : 15.84 % Favored : 82.76 % 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: 1.59 (0.24), residues: 1172 helix: 1.87 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -4.27 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 38 HIS 0.003 0.000 HIS Z 16 PHE 0.018 0.001 PHE A 113 TYR 0.011 0.001 TYR C 132 ARG 0.005 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.982 Fit side-chains REVERT: B 96 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6944 (mt-10) REVERT: B 126 MET cc_start: 0.7939 (mmm) cc_final: 0.7484 (mmt) REVERT: B 153 MET cc_start: 0.8395 (ttp) cc_final: 0.8022 (ttt) REVERT: C 93 ASN cc_start: 0.8254 (t0) cc_final: 0.8040 (t0) REVERT: D 128 ARG cc_start: 0.7657 (ttm170) cc_final: 0.7403 (ttp-110) REVERT: D 200 ARG cc_start: 0.7752 (mmm160) cc_final: 0.6969 (mtp180) outliers start: 13 outliers final: 4 residues processed: 129 average time/residue: 0.2978 time to fit residues: 49.5830 Evaluate side-chains 111 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 126 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9317 Z= 0.173 Angle : 0.484 6.778 12570 Z= 0.253 Chirality : 0.034 0.119 1465 Planarity : 0.004 0.052 1598 Dihedral : 11.769 128.123 1437 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.05 % Allowed : 16.27 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1172 helix: 2.35 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -4.08 (0.31), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.001 0.000 HIS E 233 PHE 0.014 0.001 PHE A 113 TYR 0.009 0.001 TYR B 132 ARG 0.004 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: B 96 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6939 (mt-10) REVERT: B 126 MET cc_start: 0.7854 (mmm) cc_final: 0.7211 (mmp) REVERT: B 153 MET cc_start: 0.8383 (ttp) cc_final: 0.8021 (ttt) REVERT: C 94 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5881 (tp30) REVERT: D 128 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7335 (ttp-110) REVERT: D 200 ARG cc_start: 0.7518 (mmm160) cc_final: 0.6854 (mtm-85) outliers start: 19 outliers final: 12 residues processed: 125 average time/residue: 0.2797 time to fit residues: 45.8612 Evaluate side-chains 115 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9317 Z= 0.275 Angle : 0.532 6.847 12570 Z= 0.273 Chirality : 0.037 0.180 1465 Planarity : 0.004 0.039 1598 Dihedral : 11.415 126.830 1437 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.69 % Allowed : 17.67 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.25), residues: 1172 helix: 2.37 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -3.74 (0.35), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 38 HIS 0.003 0.000 HIS Z 16 PHE 0.015 0.001 PHE A 113 TYR 0.009 0.001 TYR D 132 ARG 0.005 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 111 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7557 (m-30) cc_final: 0.7292 (m-30) REVERT: B 153 MET cc_start: 0.8407 (ttp) cc_final: 0.8045 (ttt) REVERT: D 105 GLU cc_start: 0.7698 (tp30) cc_final: 0.7480 (tp30) REVERT: D 128 ARG cc_start: 0.7763 (ttm170) cc_final: 0.7543 (ttp-110) REVERT: D 200 ARG cc_start: 0.7416 (mmm160) cc_final: 0.6813 (mtm110) outliers start: 25 outliers final: 18 residues processed: 129 average time/residue: 0.2460 time to fit residues: 42.6451 Evaluate side-chains 123 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 27 MET Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9317 Z= 0.170 Angle : 0.467 6.756 12570 Z= 0.243 Chirality : 0.034 0.143 1465 Planarity : 0.004 0.031 1598 Dihedral : 11.011 124.568 1437 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.48 % Allowed : 19.07 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.25), residues: 1172 helix: 2.67 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.68 (0.35), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.011 0.001 PHE Z 23 TYR 0.008 0.001 TYR B 132 ARG 0.004 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7526 (m-30) cc_final: 0.7269 (m-30) REVERT: B 125 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7370 (tm-30) REVERT: B 126 MET cc_start: 0.7582 (mmm) cc_final: 0.7017 (mmt) REVERT: B 153 MET cc_start: 0.8375 (ttp) cc_final: 0.8010 (ttt) REVERT: D 16 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5930 (t80) REVERT: D 128 ARG cc_start: 0.7646 (ttm170) cc_final: 0.7393 (ttp-110) REVERT: D 153 MET cc_start: 0.6909 (ttp) cc_final: 0.6627 (ttt) REVERT: D 200 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6778 (mtm110) REVERT: Z 15 MET cc_start: 0.6819 (mmt) cc_final: 0.6352 (mmt) outliers start: 23 outliers final: 15 residues processed: 125 average time/residue: 0.2658 time to fit residues: 44.0329 Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 96 GLU Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9317 Z= 0.194 Angle : 0.487 7.466 12570 Z= 0.248 Chirality : 0.035 0.120 1465 Planarity : 0.004 0.026 1598 Dihedral : 10.941 123.499 1437 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.59 % Allowed : 19.50 % Favored : 77.91 % 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: 2.88 (0.25), residues: 1172 helix: 2.71 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.57 (0.36), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 38 HIS 0.001 0.000 HIS E 233 PHE 0.014 0.001 PHE Z 23 TYR 0.007 0.001 TYR D 132 ARG 0.004 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7434 (m-30) cc_final: 0.7150 (m-30) REVERT: B 125 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 126 MET cc_start: 0.7588 (mmm) cc_final: 0.6997 (mmt) REVERT: B 153 MET cc_start: 0.8387 (ttp) cc_final: 0.8015 (ttt) REVERT: D 16 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.5920 (t80) REVERT: D 128 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7400 (ttp-110) REVERT: D 153 MET cc_start: 0.6962 (ttp) cc_final: 0.6709 (ttt) REVERT: D 200 ARG cc_start: 0.7211 (mmm160) cc_final: 0.6751 (mtm110) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.2661 time to fit residues: 47.7125 Evaluate side-chains 126 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9317 Z= 0.170 Angle : 0.478 7.517 12570 Z= 0.245 Chirality : 0.034 0.178 1465 Planarity : 0.004 0.026 1598 Dihedral : 10.747 120.701 1437 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.26 % Allowed : 20.15 % Favored : 77.59 % 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: 3.01 (0.25), residues: 1172 helix: 2.80 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.49 (0.37), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.001 0.000 HIS A 86 PHE 0.012 0.001 PHE Z 23 TYR 0.007 0.001 TYR B 132 ARG 0.004 0.000 ARG E 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.009 Fit side-chains REVERT: A 223 ASP cc_start: 0.7412 (m-30) cc_final: 0.7129 (m-30) REVERT: B 125 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7445 (tm-30) REVERT: B 126 MET cc_start: 0.7513 (mmm) cc_final: 0.6916 (mmt) REVERT: B 153 MET cc_start: 0.8365 (ttp) cc_final: 0.8002 (ttt) REVERT: D 16 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5843 (t80) REVERT: D 153 MET cc_start: 0.6969 (ttp) cc_final: 0.6703 (ttt) REVERT: D 200 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6758 (mtp180) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.2538 time to fit residues: 40.7497 Evaluate side-chains 117 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 126 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 16 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9317 Z= 0.165 Angle : 0.476 8.186 12570 Z= 0.244 Chirality : 0.034 0.123 1465 Planarity : 0.004 0.061 1598 Dihedral : 10.384 118.759 1437 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.26 % Allowed : 20.37 % 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: 3.11 (0.25), residues: 1172 helix: 2.87 (0.16), residues: 1002 sheet: None (None), residues: 0 loop : -3.42 (0.38), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 38 HIS 0.004 0.000 HIS A 86 PHE 0.014 0.001 PHE Z 23 TYR 0.007 0.001 TYR B 132 ARG 0.007 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 104 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 223 ASP cc_start: 0.7388 (m-30) cc_final: 0.7067 (m-30) REVERT: B 126 MET cc_start: 0.7429 (mmm) cc_final: 0.6924 (mmt) REVERT: B 153 MET cc_start: 0.8366 (ttp) cc_final: 0.7991 (ttt) REVERT: D 153 MET cc_start: 0.6977 (ttp) cc_final: 0.6703 (ttt) REVERT: D 200 ARG cc_start: 0.7076 (mmm160) cc_final: 0.6767 (mtp180) REVERT: Z 15 MET cc_start: 0.6976 (mmt) cc_final: 0.6430 (mmt) outliers start: 21 outliers final: 16 residues processed: 121 average time/residue: 0.2569 time to fit residues: 41.4742 Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 116 GLU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 162 THR Chi-restraints excluded: chain E residue 200 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.0020 chunk 81 optimal weight: 0.0060 chunk 31 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.0370 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN Z 16 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9317 Z= 0.134 Angle : 0.454 8.452 12570 Z= 0.236 Chirality : 0.033 0.127 1465 Planarity : 0.004 0.026 1598 Dihedral : 9.840 115.134 1437 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.51 % Allowed : 21.01 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.25), residues: 1172 helix: 3.06 (0.16), residues: 1001 sheet: None (None), residues: 0 loop : -3.35 (0.38), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 38 HIS 0.002 0.000 HIS Z 16 PHE 0.013 0.001 PHE Z 23 TYR 0.010 0.001 TYR B 132 ARG 0.005 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.028 Fit side-chains REVERT: A 150 TRP cc_start: 0.8068 (t-100) cc_final: 0.7830 (t-100) REVERT: A 223 ASP cc_start: 0.7311 (m-30) cc_final: 0.6993 (m-30) REVERT: B 125 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 126 MET cc_start: 0.7192 (mmm) cc_final: 0.6610 (mmt) REVERT: B 153 MET cc_start: 0.8263 (ttp) cc_final: 0.7898 (ttt) REVERT: C 55 LEU cc_start: 0.7907 (tp) cc_final: 0.7703 (tt) REVERT: C 64 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7622 (tm-30) REVERT: D 16 TYR cc_start: 0.6510 (OUTLIER) cc_final: 0.5732 (t80) REVERT: D 153 MET cc_start: 0.6991 (ttp) cc_final: 0.6753 (ttt) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.2252 time to fit residues: 36.2150 Evaluate side-chains 117 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 126 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0060 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 0.0980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9317 Z= 0.170 Angle : 0.467 8.523 12570 Z= 0.239 Chirality : 0.034 0.120 1465 Planarity : 0.004 0.026 1598 Dihedral : 9.679 113.143 1437 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.83 % Allowed : 20.69 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.25), residues: 1172 helix: 3.03 (0.16), residues: 1003 sheet: None (None), residues: 0 loop : -3.22 (0.39), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 38 HIS 0.001 0.000 HIS A 86 PHE 0.014 0.001 PHE Z 23 TYR 0.008 0.001 TYR B 132 ARG 0.004 0.000 ARG E 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2344 Ramachandran restraints generated. 1172 Oldfield, 0 Emsley, 1172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.986 Fit side-chains REVERT: A 150 TRP cc_start: 0.8089 (t-100) cc_final: 0.7835 (t-100) REVERT: A 223 ASP cc_start: 0.7393 (m-30) cc_final: 0.7041 (m-30) REVERT: B 126 MET cc_start: 0.7211 (mmm) cc_final: 0.6737 (mmt) REVERT: B 153 MET cc_start: 0.8253 (ttp) cc_final: 0.7886 (ttt) REVERT: C 64 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7624 (tm-30) REVERT: D 16 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5740 (t80) REVERT: D 81 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.7031 (tppt) REVERT: D 153 MET cc_start: 0.6973 (ttp) cc_final: 0.6738 (ttt) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.2340 time to fit residues: 37.9460 Evaluate side-chains 118 residues out of total 929 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 78 PHE Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain D residue 16 TYR Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain E residue 78 PHE Chi-restraints excluded: chain E residue 126 MET Chi-restraints excluded: chain E residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.163107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.124137 restraints weight = 9431.520| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.92 r_work: 0.3229 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9317 Z= 0.174 Angle : 0.473 8.475 12570 Z= 0.241 Chirality : 0.034 0.124 1465 Planarity : 0.004 0.025 1598 Dihedral : 9.610 109.166 1437 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.72 % Allowed : 21.12 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.25), residues: 1172 helix: 2.97 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -3.16 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 38 HIS 0.001 0.000 HIS B 18 PHE 0.014 0.001 PHE Z 23 TYR 0.006 0.001 TYR B 132 ARG 0.004 0.000 ARG E 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1938.90 seconds wall clock time: 35 minutes 49.90 seconds (2149.90 seconds total)