Starting phenix.real_space_refine on Wed Feb 14 13:38:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxc_24728/02_2024/7rxc_24728_updated.pdb" } resolution = 3.2 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6056 2.51 5 N 1510 2.21 5 O 1762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 175": "OD1" <-> "OD2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N GLU 101": "OE1" <-> "OE2" Residue "N ASP 109": "OD1" <-> "OD2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 208": "OD1" <-> "OD2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 404": "OE1" <-> "OE2" Residue "B TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 177": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1582 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 192} Chain breaks: 2 Chain: "L" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1588 Classifications: {'peptide': 204} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Chain: "N" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1008 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "B" Number of atoms: 3433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3433 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 24, 'TRANS': 414} Chain breaks: 4 Chain: "K" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1661 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 3, 'TRANS': 198} Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'POV': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 4, 'POV:plan-2': 4} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.64, per 1000 atoms: 0.60 Number of scatterers: 9360 At special positions: 0 Unit cell: (128.26, 125.08, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1762 8.00 N 1510 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " 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 Links applied ALPHA1-4 " GLC A 1 " - " GLC A 2 " Time building additional restraints: 3.68 Conformation dependent library (CDL) restraints added in 1.8 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 17 sheets defined 32.3% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 86 through 88 No H-bonds generated for 'chain 'L' and resid 86 through 88' Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 44 through 51 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 65 through 74 removed outlier: 4.063A pdb=" N GLY B 69 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 70 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 131 through 140 removed outlier: 4.695A pdb=" N ALA B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 165 Proline residue: B 160 - end of helix removed outlier: 4.576A pdb=" N ASP B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 201 Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 230 through 239 removed outlier: 3.868A pdb=" N SER B 234 " --> pdb=" O TRP B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 288 through 297 removed outlier: 3.868A pdb=" N ASP B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 Processing helix chain 'B' and resid 316 through 327 Processing helix chain 'B' and resid 335 through 353 removed outlier: 4.040A pdb=" N SER B 338 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA B 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 353 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 369 Processing helix chain 'B' and resid 375 through 387 Processing helix chain 'B' and resid 392 through 405 Processing helix chain 'B' and resid 503 through 516 Processing helix chain 'K' and resid 3 through 26 Processing helix chain 'K' and resid 34 through 47 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 58 through 79 Processing helix chain 'K' and resid 96 through 109 Proline residue: K 101 - end of helix Processing helix chain 'K' and resid 115 through 128 Processing helix chain 'K' and resid 130 through 141 Proline residue: K 133 - end of helix removed outlier: 3.620A pdb=" N THR K 141 " --> pdb=" O ILE K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 172 Processing helix chain 'K' and resid 178 through 201 Processing sheet with id= A, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= B, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.740A pdb=" N GLY H 33 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LEU H 45 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.891A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 161 through 164 Processing sheet with id= E, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= F, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.171A pdb=" N LYS L 108 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL L 13 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU L 110 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA L 90 " --> pdb=" O LEU L 109 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'L' and resid 119 through 123 Processing sheet with id= H, first strand: chain 'L' and resid 150 through 154 Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.170A pdb=" N THR N 118 " --> pdb=" O VAL N 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'N' and resid 115 through 117 removed outlier: 5.915A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 97 through 99 Processing sheet with id= M, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.748A pdb=" N THR B 37 " --> pdb=" O ILE B 10 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.696A pdb=" N ALA B 265 " --> pdb=" O PRO B 108 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 267 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ALA B 106 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 225 through 228 Processing sheet with id= P, first strand: chain 'B' and resid 171 through 173 removed outlier: 4.059A pdb=" N LYS B 171 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 493 through 498 418 hydrogen bonds defined for protein. 1089 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: 3.13 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1509 1.31 - 1.44: 2699 1.44 - 1.56: 5330 1.56 - 1.69: 1 1.69 - 1.81: 51 Bond restraints: 9590 Sorted by residual: bond pdb=" C29 POV K 304 " pdb="C210 POV K 304 " ideal model delta sigma weight residual 1.333 1.528 -0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.42e+01 bond pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.37e+01 bond pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 1.333 1.526 -0.193 2.00e-02 2.50e+03 9.27e+01 bond pdb=" C21 POV K 302 " pdb=" O21 POV K 302 " ideal model delta sigma weight residual 1.330 1.185 0.145 2.00e-02 2.50e+03 5.24e+01 ... (remaining 9585 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.64: 190 105.64 - 112.75: 5144 112.75 - 119.86: 3031 119.86 - 126.96: 4514 126.96 - 134.07: 126 Bond angle restraints: 13005 Sorted by residual: angle pdb=" C29 POV K 301 " pdb="C210 POV K 301 " pdb="C211 POV K 301 " ideal model delta sigma weight residual 127.67 109.02 18.65 3.00e+00 1.11e-01 3.86e+01 angle pdb=" C28 POV K 303 " pdb=" C29 POV K 303 " pdb="C210 POV K 303 " ideal model delta sigma weight residual 127.79 109.29 18.50 3.00e+00 1.11e-01 3.80e+01 angle pdb=" C28 POV K 302 " pdb=" C29 POV K 302 " pdb="C210 POV K 302 " ideal model delta sigma weight residual 127.79 109.32 18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C29 POV K 303 " pdb="C210 POV K 303 " pdb="C211 POV K 303 " ideal model delta sigma weight residual 127.67 109.31 18.36 3.00e+00 1.11e-01 3.75e+01 angle pdb=" C28 POV K 301 " pdb=" C29 POV K 301 " pdb="C210 POV K 301 " ideal model delta sigma weight residual 127.79 109.48 18.31 3.00e+00 1.11e-01 3.73e+01 ... (remaining 13000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5128 17.95 - 35.91: 428 35.91 - 53.86: 92 53.86 - 71.82: 17 71.82 - 89.77: 10 Dihedral angle restraints: 5675 sinusoidal: 2250 harmonic: 3425 Sorted by residual: dihedral pdb=" CA GLU H 158 " pdb=" C GLU H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual 180.00 148.16 31.84 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 47.49 45.51 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 58.52 34.48 1 1.00e+01 1.00e-02 1.69e+01 ... (remaining 5672 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1243 0.059 - 0.118: 181 0.118 - 0.177: 14 0.177 - 0.236: 1 0.236 - 0.294: 1 Chirality restraints: 1440 Sorted by residual: chirality pdb=" C1 GLC A 2 " pdb=" O4 GLC A 1 " pdb=" C2 GLC A 2 " pdb=" O5 GLC A 2 " both_signs ideal model delta sigma weight residual False 2.40 2.33 0.07 2.00e-02 2.50e+03 1.28e+01 chirality pdb=" C1 GLC A 1 " pdb=" C2 GLC A 1 " pdb=" O1 GLC A 1 " pdb=" O5 GLC A 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.33 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ASN B 283 " pdb=" N ASN B 283 " pdb=" C ASN B 283 " pdb=" CB ASN B 283 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1437 not shown) Planarity restraints: 1630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV K 303 " -0.278 2.00e-02 2.50e+03 2.79e-01 7.76e+02 pdb=" C29 POV K 303 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV K 303 " 0.279 2.00e-02 2.50e+03 pdb="C211 POV K 303 " -0.279 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 304 " 0.172 2.00e-02 2.50e+03 1.72e-01 2.96e+02 pdb=" C29 POV K 304 " -0.173 2.00e-02 2.50e+03 pdb="C210 POV K 304 " -0.171 2.00e-02 2.50e+03 pdb="C211 POV K 304 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV K 302 " -0.147 2.00e-02 2.50e+03 1.47e-01 2.16e+02 pdb=" C29 POV K 302 " 0.146 2.00e-02 2.50e+03 pdb="C210 POV K 302 " 0.148 2.00e-02 2.50e+03 pdb="C211 POV K 302 " -0.147 2.00e-02 2.50e+03 ... (remaining 1627 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 119 2.65 - 3.21: 8560 3.21 - 3.78: 14778 3.78 - 4.34: 20939 4.34 - 4.90: 34403 Nonbonded interactions: 78799 Sorted by model distance: nonbonded pdb=" OD1 ASP K 9 " pdb=" OH TYR K 162 " model vdw 2.089 2.440 nonbonded pdb=" OH TYR N 106 " pdb=" OD2 ASP K 9 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR K 45 " pdb=" OH TYR K 72 " model vdw 2.157 2.440 nonbonded pdb=" O ASN B 235 " pdb=" OG1 THR B 238 " model vdw 2.173 2.440 nonbonded pdb=" O PRO H 129 " pdb=" OH TYR B 513 " model vdw 2.182 2.440 ... (remaining 78794 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.200 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.110 Find NCS groups from input model: 0.290 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.006 0.195 9590 Z= 0.345 Angle : 0.777 18.648 13005 Z= 0.348 Chirality : 0.042 0.294 1440 Planarity : 0.011 0.279 1630 Dihedral : 14.270 89.769 3466 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: 1.18 (0.24), residues: 1152 helix: 1.83 (0.26), residues: 381 sheet: 0.63 (0.28), residues: 305 loop : 0.12 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 107 HIS 0.004 0.001 HIS L 95 PHE 0.030 0.001 PHE B 259 TYR 0.048 0.001 TYR K 162 ARG 0.005 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.088 Fit side-chains REVERT: N 46 GLU cc_start: 0.7803 (pt0) cc_final: 0.7590 (pt0) REVERT: K 201 LYS cc_start: 0.7742 (ttmt) cc_final: 0.7519 (ttpt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2565 time to fit residues: 50.2836 Evaluate side-chains 118 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9590 Z= 0.241 Angle : 0.526 7.778 13005 Z= 0.270 Chirality : 0.040 0.167 1440 Planarity : 0.005 0.125 1630 Dihedral : 7.174 67.473 1352 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.60 % Allowed : 7.21 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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 (0.24), residues: 1152 helix: 1.53 (0.25), residues: 386 sheet: 0.62 (0.28), residues: 305 loop : 0.15 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.005 0.001 HIS L 95 PHE 0.020 0.001 PHE B 259 TYR 0.032 0.001 TYR K 162 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 132 time to evaluate : 1.037 Fit side-chains REVERT: B 107 TYR cc_start: 0.6503 (m-80) cc_final: 0.6232 (m-80) REVERT: B 178 ASP cc_start: 0.6618 (t0) cc_final: 0.6254 (p0) REVERT: K 201 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7476 (ttpt) outliers start: 6 outliers final: 5 residues processed: 135 average time/residue: 0.2409 time to fit residues: 44.6684 Evaluate side-chains 128 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 123 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9590 Z= 0.223 Angle : 0.503 5.728 13005 Z= 0.260 Chirality : 0.039 0.170 1440 Planarity : 0.004 0.103 1630 Dihedral : 6.756 56.255 1352 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.20 % Allowed : 9.61 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: 1.05 (0.25), residues: 1152 helix: 1.54 (0.26), residues: 385 sheet: 0.60 (0.28), residues: 305 loop : 0.18 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 159 HIS 0.004 0.001 HIS L 95 PHE 0.015 0.001 PHE B 259 TYR 0.020 0.001 TYR K 162 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.048 Fit side-chains REVERT: H 153 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8147 (ttmt) REVERT: H 214 ASN cc_start: 0.8436 (t0) cc_final: 0.8031 (m-40) REVERT: L 192 GLU cc_start: 0.5996 (mm-30) cc_final: 0.5710 (tm-30) REVERT: N 46 GLU cc_start: 0.7892 (pt0) cc_final: 0.7671 (pt0) REVERT: B 23 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 107 TYR cc_start: 0.6698 (m-80) cc_final: 0.6392 (m-80) REVERT: B 178 ASP cc_start: 0.6598 (t0) cc_final: 0.6172 (p0) REVERT: B 366 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.8072 (mm-40) outliers start: 12 outliers final: 6 residues processed: 142 average time/residue: 0.2343 time to fit residues: 45.7597 Evaluate side-chains 131 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9590 Z= 0.355 Angle : 0.556 6.666 13005 Z= 0.286 Chirality : 0.041 0.202 1440 Planarity : 0.004 0.085 1630 Dihedral : 6.922 55.165 1352 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.80 % Allowed : 10.51 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.92 (0.25), residues: 1152 helix: 1.43 (0.26), residues: 386 sheet: 0.47 (0.28), residues: 306 loop : 0.14 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 32 HIS 0.008 0.001 HIS L 194 PHE 0.016 0.002 PHE B 259 TYR 0.017 0.002 TYR K 162 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8456 (t0) cc_final: 0.8037 (m-40) REVERT: L 192 GLU cc_start: 0.6079 (mm-30) cc_final: 0.5721 (tm-30) REVERT: L 193 LYS cc_start: 0.7425 (pptt) cc_final: 0.7185 (pptt) REVERT: B 23 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6391 (mp0) REVERT: B 107 TYR cc_start: 0.6755 (m-80) cc_final: 0.6402 (m-80) REVERT: B 178 ASP cc_start: 0.6623 (t0) cc_final: 0.6267 (p0) outliers start: 18 outliers final: 14 residues processed: 139 average time/residue: 0.2465 time to fit residues: 47.3835 Evaluate side-chains 145 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 9590 Z= 0.391 Angle : 0.581 7.245 13005 Z= 0.299 Chirality : 0.042 0.205 1440 Planarity : 0.004 0.062 1630 Dihedral : 7.129 58.484 1352 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.30 % Allowed : 11.21 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.79 (0.25), residues: 1152 helix: 1.37 (0.26), residues: 382 sheet: 0.30 (0.28), residues: 306 loop : 0.11 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 32 HIS 0.005 0.001 HIS L 95 PHE 0.018 0.002 PHE B 259 TYR 0.018 0.002 TYR K 76 ARG 0.003 0.001 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8506 (t0) cc_final: 0.7985 (m-40) REVERT: L 192 GLU cc_start: 0.6034 (mm-30) cc_final: 0.5669 (tm-30) REVERT: L 193 LYS cc_start: 0.7515 (pptt) cc_final: 0.7193 (pptt) REVERT: B 23 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: B 107 TYR cc_start: 0.6845 (m-80) cc_final: 0.6549 (m-80) REVERT: B 178 ASP cc_start: 0.6724 (t0) cc_final: 0.6359 (p0) REVERT: B 285 LEU cc_start: 0.7702 (tp) cc_final: 0.7489 (tt) outliers start: 23 outliers final: 18 residues processed: 145 average time/residue: 0.2371 time to fit residues: 46.8751 Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 519 VAL Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 107 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9590 Z= 0.231 Angle : 0.513 8.212 13005 Z= 0.263 Chirality : 0.040 0.232 1440 Planarity : 0.004 0.050 1630 Dihedral : 6.551 56.352 1352 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.00 % Allowed : 12.61 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.92 (0.25), residues: 1152 helix: 1.52 (0.26), residues: 383 sheet: 0.27 (0.28), residues: 312 loop : 0.25 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.004 0.001 HIS L 95 PHE 0.020 0.001 PHE K 97 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 1.030 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8509 (t0) cc_final: 0.8003 (m-40) REVERT: L 193 LYS cc_start: 0.7328 (pptt) cc_final: 0.7054 (pptt) REVERT: B 23 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: B 178 ASP cc_start: 0.6585 (t0) cc_final: 0.6245 (p0) REVERT: B 285 LEU cc_start: 0.7725 (tp) cc_final: 0.7498 (tt) REVERT: K 201 LYS cc_start: 0.7731 (ttmt) cc_final: 0.7448 (ttpt) outliers start: 20 outliers final: 16 residues processed: 143 average time/residue: 0.2342 time to fit residues: 45.8610 Evaluate side-chains 143 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 0.3980 chunk 81 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS N 97 ASN B 356 GLN B 366 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9590 Z= 0.208 Angle : 0.508 9.088 13005 Z= 0.260 Chirality : 0.039 0.232 1440 Planarity : 0.004 0.041 1630 Dihedral : 6.283 54.858 1352 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.10 % Allowed : 12.61 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1152 helix: 1.57 (0.26), residues: 382 sheet: 0.30 (0.28), residues: 311 loop : 0.28 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS L 95 PHE 0.016 0.001 PHE K 97 TYR 0.018 0.001 TYR K 76 ARG 0.002 0.000 ARG L 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8478 (t0) cc_final: 0.8001 (m-40) REVERT: L 193 LYS cc_start: 0.7374 (pptt) cc_final: 0.7127 (pptt) REVERT: B 23 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: B 107 TYR cc_start: 0.6871 (m-80) cc_final: 0.6362 (m-80) REVERT: B 178 ASP cc_start: 0.6584 (t0) cc_final: 0.6206 (p0) REVERT: B 285 LEU cc_start: 0.7695 (tp) cc_final: 0.7493 (tt) REVERT: B 323 GLU cc_start: 0.6391 (pt0) cc_final: 0.6185 (pt0) REVERT: B 336 GLN cc_start: 0.7901 (mp10) cc_final: 0.7611 (mm-40) REVERT: K 201 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7461 (ttpt) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.2363 time to fit residues: 44.9400 Evaluate side-chains 141 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 108 TYR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 100 optimal weight: 0.0170 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN B 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9590 Z= 0.312 Angle : 0.550 9.538 13005 Z= 0.279 Chirality : 0.041 0.215 1440 Planarity : 0.004 0.039 1630 Dihedral : 6.349 54.744 1352 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.30 % Allowed : 12.61 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.87 (0.25), residues: 1152 helix: 1.52 (0.26), residues: 382 sheet: 0.21 (0.28), residues: 312 loop : 0.19 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 32 HIS 0.005 0.001 HIS L 95 PHE 0.021 0.002 PHE K 97 TYR 0.014 0.001 TYR K 158 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8476 (t0) cc_final: 0.7947 (m-40) REVERT: B 23 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 107 TYR cc_start: 0.6908 (m-80) cc_final: 0.6402 (m-80) REVERT: B 178 ASP cc_start: 0.6610 (t0) cc_final: 0.6290 (p0) REVERT: B 323 GLU cc_start: 0.6459 (pt0) cc_final: 0.6233 (pt0) REVERT: B 336 GLN cc_start: 0.7920 (mp10) cc_final: 0.7622 (mm-40) REVERT: K 201 LYS cc_start: 0.7748 (ttmt) cc_final: 0.7460 (ttpt) outliers start: 23 outliers final: 19 residues processed: 139 average time/residue: 0.2314 time to fit residues: 44.3511 Evaluate side-chains 143 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain B residue 12 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 0.0270 chunk 31 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 97 ASN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9590 Z= 0.198 Angle : 0.515 10.106 13005 Z= 0.263 Chirality : 0.039 0.227 1440 Planarity : 0.003 0.039 1630 Dihedral : 6.066 53.254 1352 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.90 % Allowed : 13.61 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1152 helix: 1.62 (0.26), residues: 382 sheet: 0.30 (0.28), residues: 311 loop : 0.25 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.006 0.001 HIS L 194 PHE 0.021 0.001 PHE K 97 TYR 0.014 0.001 TYR B 525 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8467 (t0) cc_final: 0.7949 (m-40) REVERT: L 193 LYS cc_start: 0.7669 (pptt) cc_final: 0.7051 (pttt) REVERT: B 23 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: B 107 TYR cc_start: 0.6836 (m-80) cc_final: 0.6332 (m-80) REVERT: B 178 ASP cc_start: 0.6572 (t0) cc_final: 0.6186 (p0) REVERT: B 285 LEU cc_start: 0.7631 (tp) cc_final: 0.7419 (tt) REVERT: B 323 GLU cc_start: 0.6485 (pt0) cc_final: 0.6148 (pt0) REVERT: B 336 GLN cc_start: 0.7894 (mp10) cc_final: 0.7599 (mm-40) REVERT: K 201 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7448 (ttpt) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.2315 time to fit residues: 44.6861 Evaluate side-chains 143 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 ASN N 97 ASN B 87 GLN B 366 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.101 9590 Z= 0.567 Angle : 0.686 10.565 13005 Z= 0.348 Chirality : 0.046 0.234 1440 Planarity : 0.005 0.050 1630 Dihedral : 7.019 58.588 1352 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.40 % Allowed : 12.91 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.51 (0.24), residues: 1152 helix: 1.22 (0.26), residues: 381 sheet: 0.10 (0.28), residues: 309 loop : -0.08 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 32 HIS 0.006 0.001 HIS L 95 PHE 0.021 0.002 PHE B 259 TYR 0.023 0.002 TYR K 158 ARG 0.005 0.001 ARG B 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: H 214 ASN cc_start: 0.8504 (t0) cc_final: 0.7939 (m-40) REVERT: L 152 GLN cc_start: 0.6178 (mm-40) cc_final: 0.5971 (mm-40) REVERT: L 193 LYS cc_start: 0.7711 (pptt) cc_final: 0.7021 (pttt) REVERT: B 23 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6387 (mp0) REVERT: B 178 ASP cc_start: 0.6787 (t0) cc_final: 0.6451 (p0) REVERT: B 403 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8376 (t0) outliers start: 24 outliers final: 21 residues processed: 136 average time/residue: 0.2364 time to fit residues: 44.2193 Evaluate side-chains 141 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 131 VAL Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 169 THR Chi-restraints excluded: chain L residue 181 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 366 GLN Chi-restraints excluded: chain B residue 403 ASN Chi-restraints excluded: chain B residue 496 THR Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 53 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107583 restraints weight = 12134.354| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.08 r_work: 0.3082 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9590 Z= 0.228 Angle : 0.549 10.714 13005 Z= 0.280 Chirality : 0.041 0.231 1440 Planarity : 0.004 0.040 1630 Dihedral : 6.491 56.253 1352 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.80 % Allowed : 13.41 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 0.76 (0.25), residues: 1152 helix: 1.47 (0.26), residues: 380 sheet: 0.11 (0.28), residues: 311 loop : 0.13 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 159 HIS 0.005 0.001 HIS L 194 PHE 0.022 0.001 PHE K 97 TYR 0.014 0.001 TYR B 525 ARG 0.004 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.92 seconds wall clock time: 43 minutes 35.72 seconds (2615.72 seconds total)