Starting phenix.real_space_refine (version: dev) on Fri Feb 17 14:22:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/02_2023/6xi8_22191_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/02_2023/6xi8_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_22191/02_2023/6xi8_22191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/02_2023/6xi8_22191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/02_2023/6xi8_22191_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xi8_22191/02_2023/6xi8_22191_updated.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 3.23, per 1000 atoms: 0.64 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: 2.38 Conformation dependent library (CDL) restraints added in 751.4 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: 0.48 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: 1.10 Time building geometry restraints manager: 2.29 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 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. 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 2.890 Check model and map are aligned: 0.060 Process input model: 16.940 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 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 : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer Outliers : 0.77 % 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 *********************** 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 : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 185 average time/residue: 0.2109 time to fit residues: 47.6087 Evaluate side-chains 167 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.639 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8374 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 54 GLN B 212 HIS B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5762 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 5136 Z= 0.271 Angle : 0.806 10.501 6974 Z= 0.403 Chirality : 0.053 0.473 790 Planarity : 0.008 0.070 881 Dihedral : 8.880 164.157 697 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 3.09 % 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: -3.33 (0.30), residues: 621 helix: -2.03 (0.27), residues: 280 sheet: -2.46 (1.04), residues: 24 loop : -2.33 (0.33), residues: 317 *********************** 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 182 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 0.2236 time to fit residues: 46.5086 Evaluate side-chains 172 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.545 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0752 time to fit residues: 1.8962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 175 ASN B 212 HIS B 219 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5136 Z= 0.227 Angle : 0.738 10.602 6974 Z= 0.373 Chirality : 0.048 0.186 790 Planarity : 0.007 0.067 881 Dihedral : 8.374 154.305 697 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 3.47 % 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: -2.92 (0.30), residues: 621 helix: -1.45 (0.28), residues: 271 sheet: -2.81 (0.86), residues: 30 loop : -2.28 (0.33), residues: 320 *********************** 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 198 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 180 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 185 average time/residue: 0.2052 time to fit residues: 46.5803 Evaluate side-chains 181 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 0.531 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0996 time to fit residues: 2.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.4170 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 : 0.738 13.480 6974 Z= 0.363 Chirality : 0.048 0.186 790 Planarity : 0.006 0.060 881 Dihedral : 7.803 140.694 697 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer Outliers : 2.70 % 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: -2.62 (0.31), residues: 621 helix: -1.11 (0.30), residues: 270 sheet: -2.71 (0.89), residues: 30 loop : -2.20 (0.33), residues: 321 *********************** 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 183 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 174 average time/residue: 0.1899 time to fit residues: 40.8310 Evaluate side-chains 173 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0505 time to fit residues: 1.5838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 0 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 283 GLN B 219 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5833 moved from start: 0.4577 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= 0.189 Angle : 0.719 11.371 6974 Z= 0.351 Chirality : 0.046 0.171 790 Planarity : 0.006 0.061 881 Dihedral : 7.296 125.422 697 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 2.12 % 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: -2.30 (0.32), residues: 621 helix: -0.82 (0.30), residues: 268 sheet: -2.39 (0.97), residues: 30 loop : -2.07 (0.33), residues: 323 *********************** 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 191 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 182 average time/residue: 0.1845 time to fit residues: 41.7073 Evaluate side-chains 184 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0602 time to fit residues: 1.3713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.3980 chunk 12 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN A 283 GLN B 212 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5914 moved from start: 0.5023 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= 0.231 Angle : 0.764 10.040 6974 Z= 0.381 Chirality : 0.048 0.172 790 Planarity : 0.006 0.054 881 Dihedral : 7.031 111.363 697 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 2.32 % 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: -2.38 (0.32), residues: 621 helix: -0.89 (0.30), residues: 286 sheet: -2.41 (1.00), residues: 30 loop : -2.17 (0.34), residues: 305 *********************** 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 204 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 192 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 195 average time/residue: 0.1888 time to fit residues: 46.0264 Evaluate side-chains 197 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 0.569 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0528 time to fit residues: 1.4715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 38 optimal weight: 0.0470 chunk 37 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- 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 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5955 moved from start: 0.5458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 5136 Z= 0.264 Angle : 0.821 12.921 6974 Z= 0.402 Chirality : 0.051 0.319 790 Planarity : 0.006 0.052 881 Dihedral : 6.925 102.744 697 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer Outliers : 2.32 % 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: -2.50 (0.32), residues: 621 helix: -0.93 (0.30), residues: 286 sheet: -2.47 (1.01), residues: 30 loop : -2.30 (0.33), residues: 305 *********************** 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 197 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 0.579 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 186 average time/residue: 0.1965 time to fit residues: 45.1407 Evaluate side-chains 189 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 0.544 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0576 time to fit residues: 1.4655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.0040 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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: 0.5874 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 5136 Z= 0.214 Angle : 0.835 11.752 6974 Z= 0.408 Chirality : 0.050 0.343 790 Planarity : 0.006 0.051 881 Dihedral : 6.672 97.390 697 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 2.12 % 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: -2.34 (0.32), residues: 621 helix: -0.75 (0.30), residues: 280 sheet: -2.52 (0.97), residues: 30 loop : -2.23 (0.33), residues: 311 *********************** 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 197 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 186 time to evaluate : 0.593 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 188 average time/residue: 0.1857 time to fit residues: 43.5964 Evaluate side-chains 192 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 183 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0862 time to fit residues: 2.0451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.5914 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5136 Z= 0.241 Angle : 0.840 11.857 6974 Z= 0.415 Chirality : 0.052 0.383 790 Planarity : 0.006 0.062 881 Dihedral : 6.674 91.909 697 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 0.77 % 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: -2.31 (0.33), residues: 621 helix: -0.73 (0.31), residues: 283 sheet: -2.48 (1.01), residues: 30 loop : -2.22 (0.34), residues: 308 *********************** 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 189 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 185 average time/residue: 0.1999 time to fit residues: 45.8045 Evaluate side-chains 184 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 181 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1999 time to fit residues: 1.5844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 49 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 0.0010 chunk 30 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 0.0000 chunk 7 optimal weight: 0.7980 overall best weight: 0.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 5136 Z= 0.217 Angle : 0.856 11.108 6974 Z= 0.416 Chirality : 0.051 0.397 790 Planarity : 0.006 0.049 881 Dihedral : 6.585 89.283 697 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.97 % 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: -2.42 (0.32), residues: 621 helix: -0.85 (0.30), residues: 288 sheet: -2.88 (0.86), residues: 30 loop : -2.22 (0.35), residues: 303 ********************** 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 188 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 184 average time/residue: 0.1890 time to fit residues: 43.4780 Evaluate side-chains 182 residues out of total 571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0541 time to fit residues: 1.1710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 164 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.154448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.132184 restraints weight = 10095.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.136307 restraints weight = 6045.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.139095 restraints weight = 4086.567| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4298 r_free = 0.4298 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4298 r_free = 0.4298 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.6249 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= 0.220 Angle : 0.828 10.973 6974 Z= 0.406 Chirality : 0.051 0.390 790 Planarity : 0.006 0.049 881 Dihedral : 6.526 87.219 697 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 0.97 % 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: -2.43 (0.32), residues: 621 helix: -0.80 (0.29), residues: 288 sheet: -2.72 (0.89), residues: 30 loop : -2.32 (0.34), residues: 303 =============================================================================== Job complete usr+sys time: 1588.42 seconds wall clock time: 29 minutes 29.19 seconds (1769.19 seconds total)