Starting phenix.real_space_refine on Sun Mar 10 21:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/03_2024/6xi8_22191_updated.pdb" } resolution = 3.64 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 3 5.49 5 S 24 5.16 5 C 3229 2.51 5 N 836 2.21 5 O 926 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ASP 288": "OD1" <-> "OD2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B GLU 111": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ASP 192": "OD1" <-> "OD2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B ARG 281": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5022 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 499 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "A" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2342 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2150 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 10, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 101 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.17, per 1000 atoms: 0.63 Number of scatterers: 5022 At special positions: 0 Unit cell: (96.28, 85.49, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 24 16.00 P 3 15.00 Al 1 13.00 F 3 9.00 O 926 8.00 N 836 7.00 C 3229 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=0, symmetry=0 Time building additional restraints: 1.83 Conformation dependent library (CDL) restraints added in 887.5 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 1 sheets defined 43.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 289 through 294 removed outlier: 3.577A pdb=" N ALA C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 294' Processing helix chain 'C' and resid 298 through 310 removed outlier: 3.657A pdb=" N THR C 307 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 308 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 55 removed outlier: 4.510A pdb=" N GLU A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 105 through 122 removed outlier: 4.320A pdb=" N TRP A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 184 through 200 removed outlier: 3.967A pdb=" N ASP A 187 " --> pdb=" O SER A 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TRP A 189 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 190 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 200 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 263 through 270 Processing helix chain 'B' and resid 53 through 56 No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 62 through 74 Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 109 through 130 removed outlier: 5.504A pdb=" N LEU B 114 " --> pdb=" O MET B 110 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.109A pdb=" N GLU B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 173 removed outlier: 3.810A pdb=" N VAL B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N HIS B 164 " --> pdb=" O LYS B 160 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 167 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 214 through 221 Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.594A pdb=" N VAL B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 228' Processing helix chain 'B' and resid 236 through 239 No H-bonds generated for 'chain 'B' and resid 236 through 239' Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.685A pdb=" N LEU B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE B 273 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 286 removed outlier: 3.932A pdb=" N THR B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 Processing helix chain 'B' and resid 352 through 358 removed outlier: 3.612A pdb=" N LYS B 356 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 358 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 removed outlier: 3.884A pdb=" N VAL A 20 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 37 " --> pdb=" O VAL A 20 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 132 hydrogen bonds defined for protein. 363 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: 1.15 Time building geometry restraints manager: 2.01 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: 823 1.31 - 1.44: 1360 1.44 - 1.56: 2900 1.56 - 1.69: 10 1.69 - 1.81: 43 Bond restraints: 5136 Sorted by residual: bond pdb=" C THR B 351 " pdb=" N GLU B 352 " ideal model delta sigma weight residual 1.333 1.554 -0.222 1.45e-02 4.76e+03 2.34e+02 bond pdb=" C1' ADP A 401 " pdb=" C2' ADP A 401 " ideal model delta sigma weight residual 1.524 1.301 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C1' ADP A 401 " pdb=" O4' ADP A 401 " ideal model delta sigma weight residual 1.426 1.629 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.27e-02 6.20e+03 8.97e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 5131 not shown) Histogram of bond angle deviations from ideal: 78.53 - 91.43: 6 91.43 - 104.34: 96 104.34 - 117.25: 3486 117.25 - 130.16: 3349 130.16 - 143.07: 37 Bond angle restraints: 6974 Sorted by residual: angle pdb=" O GLU B 344 " pdb=" C GLU B 344 " pdb=" N ASP B 345 " ideal model delta sigma weight residual 122.43 85.70 36.73 1.46e+00 4.69e-01 6.33e+02 angle pdb=" N ASP A 228 " pdb=" CA ASP A 228 " pdb=" C ASP A 228 " ideal model delta sigma weight residual 112.04 143.07 -31.03 1.44e+00 4.82e-01 4.64e+02 angle pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" C PHE B 177 " ideal model delta sigma weight residual 111.92 128.88 -16.96 1.34e+00 5.57e-01 1.60e+02 angle pdb=" C ASP A 228 " pdb=" CA ASP A 228 " pdb=" CB ASP A 228 " ideal model delta sigma weight residual 110.56 88.32 22.24 1.83e+00 2.99e-01 1.48e+02 angle pdb=" O2P TPO A 162 " pdb=" P TPO A 162 " pdb=" O3P TPO A 162 " ideal model delta sigma weight residual 113.68 78.53 35.15 3.00e+00 1.11e-01 1.37e+02 ... (remaining 6969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.62: 3010 32.62 - 65.23: 76 65.23 - 97.85: 4 97.85 - 130.47: 0 130.47 - 163.08: 1 Dihedral angle restraints: 3091 sinusoidal: 1201 harmonic: 1890 Sorted by residual: dihedral pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual 122.80 167.25 -44.45 0 2.50e+00 1.60e-01 3.16e+02 dihedral pdb=" C PHE B 177 " pdb=" N PHE B 177 " pdb=" CA PHE B 177 " pdb=" CB PHE B 177 " ideal model delta harmonic sigma weight residual -122.60 -166.09 43.49 0 2.50e+00 1.60e-01 3.03e+02 dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 136.92 163.08 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 3088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.402: 785 0.402 - 0.803: 4 0.803 - 1.205: 0 1.205 - 1.607: 0 1.607 - 2.008: 1 Chirality restraints: 790 Sorted by residual: chirality pdb=" CA PHE B 177 " pdb=" N PHE B 177 " pdb=" C PHE B 177 " pdb=" CB PHE B 177 " both_signs ideal model delta sigma weight residual False 2.51 0.50 2.01 2.00e-01 2.50e+01 1.01e+02 chirality pdb=" CA ASP A 228 " pdb=" N ASP A 228 " pdb=" C ASP A 228 " pdb=" CB ASP A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA TYR B 362 " pdb=" N TYR B 362 " pdb=" C TYR B 362 " pdb=" CB TYR B 362 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 787 not shown) Planarity restraints: 881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 344 " -0.123 2.00e-02 2.50e+03 1.90e-01 3.61e+02 pdb=" C GLU B 344 " 0.328 2.00e-02 2.50e+03 pdb=" O GLU B 344 " -0.112 2.00e-02 2.50e+03 pdb=" N ASP B 345 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 351 " -0.061 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C THR B 351 " 0.183 2.00e-02 2.50e+03 pdb=" O THR B 351 " -0.069 2.00e-02 2.50e+03 pdb=" N GLU B 352 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 58 " -0.039 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP B 58 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP B 58 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP B 58 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 58 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP B 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 58 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 58 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 58 " -0.003 2.00e-02 2.50e+03 ... (remaining 878 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.05: 1 2.05 - 2.76: 686 2.76 - 3.47: 6755 3.47 - 4.19: 11420 4.19 - 4.90: 19696 Nonbonded interactions: 38558 Sorted by model distance: nonbonded pdb=" O CYS B 364 " pdb=" CG PRO B 367 " model vdw 1.333 3.440 nonbonded pdb=" C CYS B 364 " pdb=" CG PRO B 367 " model vdw 2.113 3.670 nonbonded pdb=" O CYS B 364 " pdb=" CD PRO B 367 " model vdw 2.160 3.440 nonbonded pdb=" CG PRO A 224 " pdb=" SD MET A 273 " model vdw 2.205 3.800 nonbonded pdb=" O GLU B 344 " pdb=" N CYS B 346 " model vdw 2.215 2.520 ... (remaining 38553 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=0.77 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 2.530 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 16.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 0.010 0.223 5136 Z= 0.688 Angle : 1.686 36.730 6974 Z= 0.897 Chirality : 0.111 2.008 790 Planarity : 0.012 0.190 881 Dihedral : 15.204 163.082 1859 Min Nonbonded Distance : 1.333 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 0.77 % Allowed : 1.35 % Favored : 97.88 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 3.03 % 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: -4.62 (0.27), residues: 621 helix: -3.24 (0.21), residues: 289 sheet: -3.17 (0.77), residues: 35 loop : -2.79 (0.31), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.006 TRP B 58 HIS 0.008 0.001 HIS A 121 PHE 0.028 0.003 PHE B 177 TYR 0.056 0.003 TYR A 57 ARG 0.013 0.001 ARG B 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7274 (m-80) cc_final: 0.6975 (m-80) REVERT: A 47 LEU cc_start: 0.7122 (mp) cc_final: 0.6829 (mp) REVERT: A 56 LYS cc_start: 0.7179 (ptmt) cc_final: 0.6933 (pttt) REVERT: A 266 PHE cc_start: 0.7276 (p90) cc_final: 0.6101 (p90) REVERT: B 122 LYS cc_start: 0.7715 (tptt) cc_final: 0.7086 (tptp) REVERT: B 145 PHE cc_start: 0.6492 (t80) cc_final: 0.5935 (t80) REVERT: B 173 SER cc_start: 0.8682 (t) cc_final: 0.8273 (t) REVERT: B 221 PHE cc_start: 0.6836 (m-10) cc_final: 0.6629 (m-80) REVERT: B 261 TYR cc_start: 0.5351 (m-80) cc_final: 0.5020 (m-80) REVERT: B 280 THR cc_start: 0.7529 (m) cc_final: 0.6935 (m) outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.2010 time to fit residues: 45.4144 Evaluate side-chains 168 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 HIS B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5136 Z= 0.221 Angle : 0.776 9.770 6974 Z= 0.385 Chirality : 0.050 0.330 790 Planarity : 0.007 0.069 881 Dihedral : 8.883 165.280 697 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.32 % Allowed : 12.74 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -3.44 (0.30), residues: 621 helix: -2.10 (0.26), residues: 279 sheet: -2.77 (0.83), residues: 34 loop : -2.35 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 58 HIS 0.004 0.001 HIS B 213 PHE 0.024 0.002 PHE A 266 TYR 0.023 0.002 TYR B 261 ARG 0.002 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.6802 (mmt) cc_final: 0.6598 (mmt) REVERT: A 266 PHE cc_start: 0.7609 (p90) cc_final: 0.6825 (p90) REVERT: B 66 GLN cc_start: 0.7016 (tp-100) cc_final: 0.6812 (tp-100) REVERT: B 112 GLU cc_start: 0.6082 (tp30) cc_final: 0.5643 (tp30) REVERT: B 122 LYS cc_start: 0.8008 (tptt) cc_final: 0.7766 (tptt) REVERT: B 125 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7166 (tm-30) REVERT: B 145 PHE cc_start: 0.6652 (t80) cc_final: 0.6432 (t80) REVERT: B 174 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7142 (pt0) REVERT: B 219 HIS cc_start: 0.6409 (OUTLIER) cc_final: 0.5820 (t70) outliers start: 12 outliers final: 8 residues processed: 174 average time/residue: 0.2023 time to fit residues: 42.9510 Evaluate side-chains 174 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 0.0030 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 GLN B 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5136 Z= 0.216 Angle : 0.707 8.640 6974 Z= 0.359 Chirality : 0.047 0.169 790 Planarity : 0.006 0.061 881 Dihedral : 8.259 155.295 697 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.47 % Allowed : 18.34 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.89 (0.31), residues: 621 helix: -1.47 (0.29), residues: 273 sheet: -2.66 (0.89), residues: 30 loop : -2.25 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 58 HIS 0.025 0.002 HIS B 219 PHE 0.023 0.002 PHE A 266 TYR 0.018 0.002 TYR B 49 ARG 0.003 0.001 ARG A 168 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 169 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7476 (m-80) cc_final: 0.6825 (m-80) REVERT: A 110 MET cc_start: 0.7779 (mmm) cc_final: 0.7365 (mmm) REVERT: A 114 LEU cc_start: 0.8458 (mm) cc_final: 0.8063 (mm) REVERT: A 115 ARG cc_start: 0.6824 (mtt-85) cc_final: 0.6493 (mtp180) REVERT: A 266 PHE cc_start: 0.7786 (p90) cc_final: 0.7407 (p90) REVERT: B 66 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6800 (tp-100) REVERT: B 122 LYS cc_start: 0.8089 (tptt) cc_final: 0.7855 (tptt) REVERT: B 125 GLN cc_start: 0.7555 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 145 PHE cc_start: 0.6768 (t80) cc_final: 0.6560 (t80) REVERT: B 191 ARG cc_start: 0.7120 (ttt180) cc_final: 0.6710 (ttt180) REVERT: B 219 HIS cc_start: 0.6350 (OUTLIER) cc_final: 0.5700 (t-90) REVERT: B 221 PHE cc_start: 0.7247 (m-10) cc_final: 0.7028 (m-80) outliers start: 18 outliers final: 9 residues processed: 175 average time/residue: 0.2045 time to fit residues: 43.6261 Evaluate side-chains 178 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN B 212 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5136 Z= 0.181 Angle : 0.690 8.787 6974 Z= 0.344 Chirality : 0.046 0.180 790 Planarity : 0.006 0.061 881 Dihedral : 7.646 139.872 697 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.05 % Allowed : 22.20 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.69 (0.31), residues: 621 helix: -1.22 (0.29), residues: 278 sheet: -2.59 (0.91), residues: 30 loop : -2.22 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 58 HIS 0.009 0.001 HIS B 219 PHE 0.020 0.002 PHE A 266 TYR 0.019 0.001 TYR B 55 ARG 0.004 0.000 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7444 (m-80) cc_final: 0.6729 (m-80) REVERT: A 56 LYS cc_start: 0.7127 (pttp) cc_final: 0.6736 (pttt) REVERT: A 74 MET cc_start: 0.7348 (tpp) cc_final: 0.7115 (tpp) REVERT: A 110 MET cc_start: 0.7777 (mmm) cc_final: 0.7440 (tpt) REVERT: A 115 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6608 (mtp180) REVERT: A 123 ASN cc_start: 0.6855 (m-40) cc_final: 0.6650 (m-40) REVERT: B 122 LYS cc_start: 0.8068 (tptt) cc_final: 0.7801 (tptt) REVERT: B 125 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 169 LEU cc_start: 0.7994 (tp) cc_final: 0.7583 (mt) REVERT: B 219 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.6247 (t70) REVERT: B 221 PHE cc_start: 0.7284 (m-10) cc_final: 0.7014 (m-10) REVERT: B 248 ARG cc_start: 0.7158 (mtp85) cc_final: 0.6900 (mtp85) REVERT: B 275 ASP cc_start: 0.4665 (t0) cc_final: 0.4440 (t0) outliers start: 21 outliers final: 15 residues processed: 176 average time/residue: 0.1965 time to fit residues: 42.9378 Evaluate side-chains 178 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 0.0570 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5136 Z= 0.268 Angle : 0.738 9.064 6974 Z= 0.373 Chirality : 0.049 0.195 790 Planarity : 0.006 0.060 881 Dihedral : 7.241 121.101 697 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 5.21 % Allowed : 22.59 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.73 (0.31), residues: 621 helix: -1.21 (0.29), residues: 276 sheet: -2.27 (0.99), residues: 30 loop : -2.34 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 58 HIS 0.019 0.002 HIS B 219 PHE 0.035 0.002 PHE B 145 TYR 0.014 0.001 TYR B 55 ARG 0.005 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7567 (m-80) cc_final: 0.7125 (m-80) REVERT: A 110 MET cc_start: 0.7917 (mmm) cc_final: 0.7631 (tpt) REVERT: A 115 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6788 (mtp180) REVERT: B 112 GLU cc_start: 0.6199 (tp30) cc_final: 0.5772 (tp30) REVERT: B 122 LYS cc_start: 0.8161 (tptt) cc_final: 0.7924 (tptt) REVERT: B 125 GLN cc_start: 0.7676 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 145 PHE cc_start: 0.7158 (t80) cc_final: 0.6870 (t80) REVERT: B 155 MET cc_start: 0.6089 (ptt) cc_final: 0.5879 (ptt) REVERT: B 169 LEU cc_start: 0.8059 (tp) cc_final: 0.7735 (mt) REVERT: B 191 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6760 (ttt180) REVERT: B 247 LYS cc_start: 0.8058 (mttp) cc_final: 0.7807 (mttp) REVERT: B 331 LYS cc_start: 0.8235 (mtmm) cc_final: 0.8008 (mtmm) REVERT: B 338 GLU cc_start: 0.6787 (pp20) cc_final: 0.6543 (pp20) outliers start: 27 outliers final: 20 residues processed: 181 average time/residue: 0.1879 time to fit residues: 42.1826 Evaluate side-chains 188 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5136 Z= 0.238 Angle : 0.739 12.067 6974 Z= 0.371 Chirality : 0.049 0.200 790 Planarity : 0.006 0.052 881 Dihedral : 6.898 105.661 697 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.60 % Allowed : 25.68 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.68 (0.31), residues: 621 helix: -1.14 (0.29), residues: 277 sheet: -2.33 (1.02), residues: 30 loop : -2.34 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 58 HIS 0.006 0.001 HIS A 121 PHE 0.028 0.002 PHE B 145 TYR 0.047 0.002 TYR A 204 ARG 0.005 0.000 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7586 (m-80) cc_final: 0.7148 (m-80) REVERT: A 56 LYS cc_start: 0.7108 (pttp) cc_final: 0.6580 (pttt) REVERT: A 110 MET cc_start: 0.7901 (mmm) cc_final: 0.7569 (tpt) REVERT: A 115 ARG cc_start: 0.7028 (mtt-85) cc_final: 0.6813 (mtp180) REVERT: B 112 GLU cc_start: 0.6248 (tp30) cc_final: 0.5815 (tp30) REVERT: B 122 LYS cc_start: 0.8157 (tptt) cc_final: 0.7909 (tptt) REVERT: B 125 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 145 PHE cc_start: 0.7056 (t80) cc_final: 0.6797 (t80) REVERT: B 169 LEU cc_start: 0.8030 (tp) cc_final: 0.7743 (mt) REVERT: B 247 LYS cc_start: 0.8033 (mttp) cc_final: 0.7784 (mttp) REVERT: B 275 ASP cc_start: 0.4997 (t0) cc_final: 0.4686 (t0) outliers start: 29 outliers final: 23 residues processed: 187 average time/residue: 0.1881 time to fit residues: 43.6093 Evaluate side-chains 197 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 268 CYS Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 37 optimal weight: 0.0030 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5136 Z= 0.194 Angle : 0.731 10.744 6974 Z= 0.363 Chirality : 0.048 0.197 790 Planarity : 0.006 0.056 881 Dihedral : 6.605 99.826 697 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 4.44 % Allowed : 28.76 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.32), residues: 621 helix: -0.87 (0.30), residues: 265 sheet: -2.43 (0.97), residues: 30 loop : -2.11 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.034 0.002 PHE B 145 TYR 0.022 0.001 TYR A 204 ARG 0.005 0.001 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 178 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7481 (m-80) cc_final: 0.7186 (m-80) REVERT: A 56 LYS cc_start: 0.7062 (pttp) cc_final: 0.6689 (pttt) REVERT: A 61 MET cc_start: 0.6273 (mmm) cc_final: 0.5946 (mmt) REVERT: A 74 MET cc_start: 0.7503 (tpp) cc_final: 0.7264 (tpp) REVERT: A 110 MET cc_start: 0.7798 (mmm) cc_final: 0.7526 (tpt) REVERT: A 121 HIS cc_start: 0.7597 (m90) cc_final: 0.7395 (m90) REVERT: B 66 GLN cc_start: 0.7107 (tp-100) cc_final: 0.6820 (tp-100) REVERT: B 112 GLU cc_start: 0.6173 (tp30) cc_final: 0.5789 (tp30) REVERT: B 122 LYS cc_start: 0.8128 (tptt) cc_final: 0.7865 (tptt) REVERT: B 125 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 145 PHE cc_start: 0.6954 (t80) cc_final: 0.6620 (t80) REVERT: B 169 LEU cc_start: 0.8016 (tp) cc_final: 0.7744 (mt) REVERT: B 247 LYS cc_start: 0.8039 (mttp) cc_final: 0.7787 (mttp) outliers start: 23 outliers final: 20 residues processed: 184 average time/residue: 0.1840 time to fit residues: 42.0586 Evaluate side-chains 195 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 288 ARG Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.0060 chunk 38 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.3396 ------------------------------------------------------------------------------- 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: 0.6052 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5136 Z= 0.204 Angle : 0.756 9.667 6974 Z= 0.375 Chirality : 0.048 0.185 790 Planarity : 0.006 0.062 881 Dihedral : 6.511 96.010 697 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 3.86 % Allowed : 29.54 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.35 (0.32), residues: 621 helix: -0.79 (0.31), residues: 265 sheet: -2.67 (0.92), residues: 30 loop : -2.14 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP B 58 HIS 0.005 0.001 HIS A 121 PHE 0.041 0.002 PHE B 145 TYR 0.017 0.001 TYR A 204 ARG 0.006 0.000 ARG B 244 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 TYR cc_start: 0.7426 (m-80) cc_final: 0.7216 (m-80) REVERT: A 50 SER cc_start: 0.7510 (t) cc_final: 0.7267 (t) REVERT: A 61 MET cc_start: 0.6356 (mmm) cc_final: 0.6029 (mmt) REVERT: A 74 MET cc_start: 0.7493 (tpp) cc_final: 0.7274 (tpp) REVERT: A 110 MET cc_start: 0.7618 (mmm) cc_final: 0.7414 (tpt) REVERT: B 66 GLN cc_start: 0.7039 (tp-100) cc_final: 0.6779 (tp-100) REVERT: B 112 GLU cc_start: 0.6152 (tp30) cc_final: 0.5774 (tp30) REVERT: B 122 LYS cc_start: 0.8113 (tptt) cc_final: 0.7851 (tptt) REVERT: B 125 GLN cc_start: 0.7688 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 169 LEU cc_start: 0.8010 (tp) cc_final: 0.7753 (mt) REVERT: B 247 LYS cc_start: 0.8011 (mttp) cc_final: 0.7786 (mttp) outliers start: 20 outliers final: 18 residues processed: 185 average time/residue: 0.1785 time to fit residues: 41.3408 Evaluate side-chains 195 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 53 optimal weight: 0.0030 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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: 0.6065 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5136 Z= 0.208 Angle : 0.772 11.947 6974 Z= 0.377 Chirality : 0.050 0.348 790 Planarity : 0.006 0.051 881 Dihedral : 6.465 91.711 697 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 4.44 % Allowed : 30.50 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.44 (0.32), residues: 621 helix: -0.93 (0.31), residues: 264 sheet: -2.61 (0.94), residues: 30 loop : -2.12 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.009 0.001 HIS A 121 PHE 0.039 0.002 PHE B 145 TYR 0.026 0.001 TYR B 55 ARG 0.008 0.001 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.7566 (t) cc_final: 0.7345 (t) REVERT: A 74 MET cc_start: 0.7505 (tpp) cc_final: 0.7286 (tpp) REVERT: A 123 ASN cc_start: 0.6414 (t0) cc_final: 0.6059 (t0) REVERT: B 66 GLN cc_start: 0.7052 (tp-100) cc_final: 0.6772 (tp-100) REVERT: B 112 GLU cc_start: 0.6167 (tp30) cc_final: 0.5783 (tp30) REVERT: B 122 LYS cc_start: 0.8123 (tptt) cc_final: 0.7861 (tptt) REVERT: B 125 GLN cc_start: 0.7679 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 169 LEU cc_start: 0.8033 (tp) cc_final: 0.7771 (mt) REVERT: B 230 TYR cc_start: 0.5993 (m-80) cc_final: 0.5698 (m-80) REVERT: B 247 LYS cc_start: 0.8125 (mttp) cc_final: 0.7826 (mttp) outliers start: 23 outliers final: 22 residues processed: 181 average time/residue: 0.1865 time to fit residues: 41.9613 Evaluate side-chains 194 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5136 Z= 0.327 Angle : 0.831 9.667 6974 Z= 0.417 Chirality : 0.054 0.408 790 Planarity : 0.006 0.058 881 Dihedral : 6.889 87.706 697 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.02 % Allowed : 30.12 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.69 (0.32), residues: 621 helix: -1.14 (0.30), residues: 277 sheet: -2.79 (1.01), residues: 30 loop : -2.29 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 58 HIS 0.007 0.002 HIS A 121 PHE 0.016 0.002 PHE A 266 TYR 0.021 0.002 TYR B 55 ARG 0.008 0.001 ARG A 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 187 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.7830 (pt) cc_final: 0.7559 (pp) REVERT: B 66 GLN cc_start: 0.7192 (tp-100) cc_final: 0.6918 (tp-100) REVERT: B 112 GLU cc_start: 0.6216 (tp30) cc_final: 0.5819 (tp30) REVERT: B 122 LYS cc_start: 0.8178 (tptt) cc_final: 0.7907 (tptt) REVERT: B 125 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7349 (tm-30) REVERT: B 156 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6252 (pm20) REVERT: B 169 LEU cc_start: 0.8103 (tp) cc_final: 0.7809 (tp) outliers start: 26 outliers final: 22 residues processed: 195 average time/residue: 0.1864 time to fit residues: 45.2810 Evaluate side-chains 207 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 184 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 245 CYS Chi-restraints excluded: chain B residue 280 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.151387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.128012 restraints weight = 10089.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.132089 restraints weight = 6085.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.134986 restraints weight = 4181.551| |-----------------------------------------------------------------------------| r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5136 Z= 0.230 Angle : 0.816 10.636 6974 Z= 0.401 Chirality : 0.052 0.387 790 Planarity : 0.006 0.050 881 Dihedral : 6.670 86.938 697 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 5.02 % Allowed : 33.20 % Favored : 61.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -2.51 (0.32), residues: 621 helix: -0.94 (0.30), residues: 270 sheet: -2.89 (0.95), residues: 30 loop : -2.20 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 58 HIS 0.007 0.001 HIS A 121 PHE 0.022 0.001 PHE B 149 TYR 0.021 0.002 TYR C 277 ARG 0.008 0.001 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1642.63 seconds wall clock time: 30 minutes 17.56 seconds (1817.56 seconds total)