Starting phenix.real_space_refine on Mon Apr 8 11:19:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w9w_37383/04_2024/8w9w_37383_updated.pdb" } resolution = 3.74 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= 0.004 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 114 5.16 5 C 8972 2.51 5 N 2134 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 389": "OE1" <-> "OE2" Residue "D GLU 314": "OE1" <-> "OE2" Residue "D GLU 399": "OE1" <-> "OE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E GLU 399": "OE1" <-> "OE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13382 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2192 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'UJO': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'UJO': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'OPE': 1, 'UJO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.05, per 1000 atoms: 0.60 Number of scatterers: 13382 At special positions: 0 Unit cell: (144.1, 157.3, 80.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 4 15.00 O 2158 8.00 N 2134 7.00 C 8972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 293 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 293 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 293 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 293 " distance=2.06 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 293 " distance=2.05 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 293 " distance=2.04 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: 5.99 Conformation dependent library (CDL) restraints added in 2.5 seconds 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 0 sheets defined 53.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 149 through 175 removed outlier: 4.416A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 154 " --> pdb=" O TRP A 150 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 175 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 220 Processing helix chain 'A' and resid 225 through 249 removed outlier: 3.531A pdb=" N CYS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 282 Processing helix chain 'A' and resid 300 through 314 Processing helix chain 'A' and resid 323 through 340 Processing helix chain 'A' and resid 346 through 368 Processing helix chain 'A' and resid 386 through 389 No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'B' and resid 152 through 176 removed outlier: 3.910A pdb=" N GLU B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 220 Processing helix chain 'B' and resid 225 through 249 removed outlier: 3.577A pdb=" N CYS B 233 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 282 Processing helix chain 'B' and resid 300 through 314 Processing helix chain 'B' and resid 323 through 340 Processing helix chain 'B' and resid 346 through 369 Processing helix chain 'C' and resid 152 through 175 removed outlier: 3.796A pdb=" N GLU C 175 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 220 Processing helix chain 'C' and resid 225 through 249 removed outlier: 3.534A pdb=" N CYS C 233 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 282 Processing helix chain 'C' and resid 300 through 314 Processing helix chain 'C' and resid 323 through 340 Processing helix chain 'C' and resid 346 through 369 Processing helix chain 'C' and resid 386 through 389 No H-bonds generated for 'chain 'C' and resid 386 through 389' Processing helix chain 'D' and resid 152 through 176 removed outlier: 3.878A pdb=" N GLU D 175 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG D 176 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 220 removed outlier: 4.597A pdb=" N THR D 204 " --> pdb=" O ALA D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 249 removed outlier: 3.905A pdb=" N CYS D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 280 Processing helix chain 'D' and resid 300 through 314 Processing helix chain 'D' and resid 323 through 340 Processing helix chain 'D' and resid 346 through 369 Processing helix chain 'D' and resid 386 through 389 No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'E' and resid 152 through 175 removed outlier: 3.887A pdb=" N GLU E 175 " --> pdb=" O VAL E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 220 removed outlier: 4.313A pdb=" N THR E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 249 removed outlier: 3.797A pdb=" N CYS E 233 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 238 " --> pdb=" O SER E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 4.346A pdb=" N LEU E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N HIS E 274 " --> pdb=" O TRP E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 314 Processing helix chain 'E' and resid 323 through 341 Processing helix chain 'E' and resid 346 through 369 Processing helix chain 'E' and resid 386 through 389 No H-bonds generated for 'chain 'E' and resid 386 through 389' Processing helix chain 'F' and resid 152 through 175 removed outlier: 4.320A pdb=" N GLU F 175 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 220 removed outlier: 4.178A pdb=" N THR F 204 " --> pdb=" O ALA F 200 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU F 205 " --> pdb=" O PHE F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 249 removed outlier: 3.502A pdb=" N CYS F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 238 " --> pdb=" O SER F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 282 Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 323 through 340 Processing helix chain 'F' and resid 346 through 368 Processing helix chain 'F' and resid 386 through 389 No H-bonds generated for 'chain 'F' and resid 386 through 389' 628 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.36 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2178 1.33 - 1.47: 5831 1.47 - 1.61: 5663 1.61 - 1.76: 12 1.76 - 1.90: 168 Bond restraints: 13852 Sorted by residual: bond pdb=" CG PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 1.503 1.253 0.250 3.40e-02 8.65e+02 5.43e+01 bond pdb=" CG PRO E 403 " pdb=" CD PRO E 403 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.96e+01 bond pdb=" CB CYS E 293 " pdb=" SG CYS E 293 " ideal model delta sigma weight residual 1.808 1.687 0.121 3.30e-02 9.18e+02 1.35e+01 bond pdb=" CB MET B 285 " pdb=" CG MET B 285 " ideal model delta sigma weight residual 1.520 1.419 0.101 3.00e-02 1.11e+03 1.13e+01 bond pdb=" CB CYS D 293 " pdb=" SG CYS D 293 " ideal model delta sigma weight residual 1.808 1.699 0.109 3.30e-02 9.18e+02 1.09e+01 ... (remaining 13847 not shown) Histogram of bond angle deviations from ideal: 88.58 - 97.75: 18 97.75 - 106.93: 496 106.93 - 116.10: 8431 116.10 - 125.28: 9503 125.28 - 134.45: 380 Bond angle restraints: 18828 Sorted by residual: angle pdb=" CA PRO E 403 " pdb=" N PRO E 403 " pdb=" CD PRO E 403 " ideal model delta sigma weight residual 112.00 92.55 19.45 1.40e+00 5.10e-01 1.93e+02 angle pdb=" CA PRO D 403 " pdb=" N PRO D 403 " pdb=" CD PRO D 403 " ideal model delta sigma weight residual 112.00 92.59 19.41 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CA PRO A 195 " pdb=" N PRO A 195 " pdb=" CD PRO A 195 " ideal model delta sigma weight residual 112.00 96.41 15.59 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO B 195 " pdb=" N PRO B 195 " pdb=" CD PRO B 195 " ideal model delta sigma weight residual 112.00 96.49 15.51 1.40e+00 5.10e-01 1.23e+02 angle pdb=" N PRO D 403 " pdb=" CD PRO D 403 " pdb=" CG PRO D 403 " ideal model delta sigma weight residual 103.20 88.58 14.62 1.50e+00 4.44e-01 9.50e+01 ... (remaining 18823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 7518 33.80 - 67.60: 316 67.60 - 101.40: 24 101.40 - 135.21: 7 135.21 - 169.01: 3 Dihedral angle restraints: 7868 sinusoidal: 3200 harmonic: 4668 Sorted by residual: dihedral pdb=" CA CYS E 293 " pdb=" C CYS E 293 " pdb=" N GLY E 294 " pdb=" CA GLY E 294 " ideal model delta harmonic sigma weight residual -180.00 -153.07 -26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA CYS D 293 " pdb=" C CYS D 293 " pdb=" N GLY D 294 " pdb=" CA GLY D 294 " ideal model delta harmonic sigma weight residual -180.00 -153.49 -26.51 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" C24 UJO A 500 " pdb=" C25 UJO A 500 " pdb=" C26 UJO A 500 " pdb=" C27 UJO A 500 " ideal model delta sinusoidal sigma weight residual 139.82 -51.17 -169.01 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 7865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1950 0.094 - 0.189: 85 0.189 - 0.283: 9 0.283 - 0.377: 3 0.377 - 0.472: 5 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CB THR D 246 " pdb=" CA THR D 246 " pdb=" OG1 THR D 246 " pdb=" CG2 THR D 246 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CB ILE D 197 " pdb=" CA ILE D 197 " pdb=" CG1 ILE D 197 " pdb=" CG2 ILE D 197 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PRO C 317 " pdb=" N PRO C 317 " pdb=" C PRO C 317 " pdb=" CB PRO C 317 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 2049 not shown) Planarity restraints: 2262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 194 " 0.115 5.00e-02 4.00e+02 1.59e-01 4.06e+01 pdb=" N PRO B 195 " -0.275 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 194 " -0.111 5.00e-02 4.00e+02 1.54e-01 3.78e+01 pdb=" N PRO A 195 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO A 195 " -0.077 5.00e-02 4.00e+02 pdb=" CD PRO A 195 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 382 " 0.086 5.00e-02 4.00e+02 1.25e-01 2.49e+01 pdb=" N PRO F 383 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO F 383 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO F 383 " 0.066 5.00e-02 4.00e+02 ... (remaining 2259 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 113 2.56 - 3.15: 10714 3.15 - 3.73: 20275 3.73 - 4.32: 25540 4.32 - 4.90: 43772 Nonbonded interactions: 100414 Sorted by model distance: nonbonded pdb=" OG SER A 268 " pdb=" OE1 GLU A 271 " model vdw 1.975 2.440 nonbonded pdb=" OD2 ASP C 179 " pdb=" OG1 THR C 182 " model vdw 2.032 2.440 nonbonded pdb=" OG SER B 268 " pdb=" OE1 GLU B 271 " model vdw 2.059 2.440 nonbonded pdb=" N GLU B 271 " pdb=" OE1 GLU B 271 " model vdw 2.133 2.520 nonbonded pdb=" OD1 ASP D 188 " pdb=" N ILE D 189 " model vdw 2.175 2.520 ... (remaining 100409 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 144 through 407 or resid 500)) selection = (chain 'B' and (resid 144 through 407 or resid 500)) selection = (chain 'C' and (resid 144 through 407 or resid 500)) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 144 through 407 or resid 500)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.140 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.930 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.007 0.250 13852 Z= 0.455 Angle : 0.956 19.445 18828 Z= 0.517 Chirality : 0.052 0.472 2052 Planarity : 0.009 0.159 2262 Dihedral : 18.616 169.006 4838 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.05 % Favored : 89.76 % Rotamer: Outliers : 1.11 % Allowed : 23.37 % Favored : 75.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1572 helix: 1.57 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -2.65 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 199 HIS 0.008 0.001 HIS F 174 PHE 0.027 0.001 PHE E 201 TYR 0.038 0.002 TYR D 315 ARG 0.016 0.001 ARG F 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 381 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 GLN cc_start: 0.8019 (mm-40) cc_final: 0.7782 (mm-40) REVERT: B 190 PHE cc_start: 0.7242 (t80) cc_final: 0.6978 (t80) REVERT: B 228 LEU cc_start: 0.7830 (mt) cc_final: 0.7341 (mp) REVERT: B 264 LYS cc_start: 0.7926 (tptt) cc_final: 0.7465 (mttm) REVERT: C 151 LYS cc_start: 0.8450 (mttt) cc_final: 0.8216 (mtmt) REVERT: C 154 LEU cc_start: 0.8549 (mm) cc_final: 0.8223 (tp) REVERT: C 190 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6745 (t80) REVERT: C 241 LEU cc_start: 0.8371 (mm) cc_final: 0.7799 (tp) REVERT: D 180 MET cc_start: 0.7803 (tpp) cc_final: 0.7312 (ttt) REVERT: D 230 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7333 (mpp80) REVERT: D 272 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7134 (mttt) REVERT: D 297 MET cc_start: 0.7458 (tmm) cc_final: 0.6429 (ttm) REVERT: E 180 MET cc_start: 0.6623 (ttp) cc_final: 0.6392 (ttm) REVERT: E 183 TYR cc_start: 0.5982 (m-80) cc_final: 0.5416 (m-80) REVERT: E 217 LEU cc_start: 0.9054 (mt) cc_final: 0.8831 (mt) REVERT: E 236 MET cc_start: 0.7444 (mmm) cc_final: 0.6923 (tpp) REVERT: E 274 HIS cc_start: 0.8064 (m-70) cc_final: 0.7835 (m170) REVERT: E 336 PHE cc_start: 0.8368 (t80) cc_final: 0.8124 (t80) REVERT: F 175 GLU cc_start: 0.8099 (pp20) cc_final: 0.7629 (tp30) REVERT: F 203 MET cc_start: 0.7621 (mmp) cc_final: 0.7389 (mmm) REVERT: F 241 LEU cc_start: 0.8539 (mm) cc_final: 0.8003 (tp) outliers start: 16 outliers final: 5 residues processed: 391 average time/residue: 0.2445 time to fit residues: 139.5429 Evaluate side-chains 305 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 299 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain D residue 291 HIS Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 320 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 0.2980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN F 274 HIS F 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13852 Z= 0.260 Angle : 0.654 9.736 18828 Z= 0.337 Chirality : 0.043 0.185 2052 Planarity : 0.005 0.077 2262 Dihedral : 13.824 163.420 1910 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.92 % Favored : 90.01 % Rotamer: Outliers : 5.53 % Allowed : 20.61 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1572 helix: 1.59 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 199 HIS 0.006 0.001 HIS D 224 PHE 0.020 0.002 PHE F 201 TYR 0.015 0.002 TYR D 315 ARG 0.004 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 323 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 ILE cc_start: 0.8656 (tt) cc_final: 0.8377 (tt) REVERT: A 283 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7605 (m-10) REVERT: B 190 PHE cc_start: 0.7112 (t80) cc_final: 0.6872 (t80) REVERT: B 264 LYS cc_start: 0.7835 (tptt) cc_final: 0.7448 (mttp) REVERT: C 151 LYS cc_start: 0.8586 (mttt) cc_final: 0.8207 (mtmt) REVERT: C 190 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6808 (t80) REVERT: C 241 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7898 (tp) REVERT: C 260 GLN cc_start: 0.8232 (mp10) cc_final: 0.8011 (mp10) REVERT: D 160 PHE cc_start: 0.7830 (m-80) cc_final: 0.7526 (m-80) REVERT: D 180 MET cc_start: 0.7956 (tpp) cc_final: 0.7674 (ttt) REVERT: D 201 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.7028 (t80) REVERT: D 236 MET cc_start: 0.7550 (mmm) cc_final: 0.6937 (tpp) REVERT: D 272 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7237 (mttt) REVERT: D 274 HIS cc_start: 0.8034 (m-70) cc_final: 0.7745 (m170) REVERT: D 297 MET cc_start: 0.7894 (tmm) cc_final: 0.7007 (ttp) REVERT: E 180 MET cc_start: 0.6527 (ttp) cc_final: 0.6279 (ttt) REVERT: E 183 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5498 (m-80) REVERT: E 201 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6818 (t80) REVERT: E 205 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6941 (mt-10) REVERT: E 216 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (mm) REVERT: E 274 HIS cc_start: 0.8063 (m-70) cc_final: 0.7838 (m-70) REVERT: F 175 GLU cc_start: 0.8053 (pp20) cc_final: 0.7555 (tp30) REVERT: F 190 PHE cc_start: 0.7187 (OUTLIER) cc_final: 0.6645 (t80) REVERT: F 241 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8008 (tp) outliers start: 80 outliers final: 44 residues processed: 371 average time/residue: 0.2296 time to fit residues: 127.4276 Evaluate side-chains 348 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 295 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 261 CYS Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 201 PHE Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 320 TRP Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 0.0020 chunk 153 optimal weight: 0.0470 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.6688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 321 ASN B 393 ASN ** F 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 373 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13852 Z= 0.184 Angle : 0.592 11.441 18828 Z= 0.305 Chirality : 0.041 0.189 2052 Planarity : 0.004 0.056 2262 Dihedral : 13.097 161.422 1903 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 4.77 % Allowed : 22.54 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1572 helix: 1.76 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.73 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 320 HIS 0.013 0.001 HIS F 274 PHE 0.022 0.001 PHE E 336 TYR 0.012 0.001 TYR D 158 ARG 0.003 0.000 ARG B 318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 309 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: A 366 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7790 (mp) REVERT: B 190 PHE cc_start: 0.7086 (t80) cc_final: 0.6854 (t80) REVERT: B 264 LYS cc_start: 0.7848 (tptt) cc_final: 0.7357 (mtmm) REVERT: B 283 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7712 (m-10) REVERT: C 151 LYS cc_start: 0.8576 (mttt) cc_final: 0.8133 (mtmt) REVERT: C 154 LEU cc_start: 0.8470 (mm) cc_final: 0.8215 (tp) REVERT: C 190 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6631 (t80) REVERT: C 241 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.7891 (tp) REVERT: C 308 LEU cc_start: 0.7715 (mm) cc_final: 0.7302 (tt) REVERT: D 160 PHE cc_start: 0.7903 (m-80) cc_final: 0.7561 (m-80) REVERT: D 180 MET cc_start: 0.7883 (tpp) cc_final: 0.7269 (tmm) REVERT: D 272 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7148 (mttt) REVERT: D 297 MET cc_start: 0.7911 (tmm) cc_final: 0.6903 (ttp) REVERT: D 387 PHE cc_start: 0.7909 (t80) cc_final: 0.5609 (m-80) REVERT: E 180 MET cc_start: 0.6523 (ttp) cc_final: 0.5940 (ttt) REVERT: E 183 TYR cc_start: 0.6004 (OUTLIER) cc_final: 0.5314 (m-80) REVERT: E 201 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6537 (t80) REVERT: E 205 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6858 (mm-30) REVERT: E 236 MET cc_start: 0.7560 (mmm) cc_final: 0.6814 (tpp) REVERT: E 343 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F 175 GLU cc_start: 0.8034 (pp20) cc_final: 0.7500 (tp30) REVERT: F 236 MET cc_start: 0.7881 (mmm) cc_final: 0.7388 (mmm) REVERT: F 241 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7993 (tp) REVERT: F 308 LEU cc_start: 0.7577 (mm) cc_final: 0.7340 (tt) outliers start: 69 outliers final: 47 residues processed: 354 average time/residue: 0.2320 time to fit residues: 126.1849 Evaluate side-chains 355 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 201 PHE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 321 ASN B 398 ASN ** C 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13852 Z= 0.200 Angle : 0.595 8.887 18828 Z= 0.306 Chirality : 0.041 0.170 2052 Planarity : 0.004 0.051 2262 Dihedral : 12.764 161.157 1900 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.86 % Favored : 90.08 % Rotamer: Outliers : 5.81 % Allowed : 22.75 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1572 helix: 1.76 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 320 HIS 0.005 0.001 HIS D 224 PHE 0.024 0.001 PHE C 388 TYR 0.017 0.001 TYR C 362 ARG 0.004 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 319 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6813 (mt-10) REVERT: A 283 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: A 366 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 190 PHE cc_start: 0.7073 (t80) cc_final: 0.6851 (t80) REVERT: B 264 LYS cc_start: 0.7902 (tptt) cc_final: 0.7514 (mttp) REVERT: B 283 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7855 (m-10) REVERT: B 348 ASP cc_start: 0.7942 (m-30) cc_final: 0.7665 (m-30) REVERT: C 151 LYS cc_start: 0.8584 (mttt) cc_final: 0.8210 (mtmt) REVERT: C 154 LEU cc_start: 0.8389 (mm) cc_final: 0.8152 (tp) REVERT: C 190 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6459 (t80) REVERT: C 205 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6677 (mt-10) REVERT: C 241 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7904 (tp) REVERT: C 308 LEU cc_start: 0.7756 (mm) cc_final: 0.7321 (tt) REVERT: D 180 MET cc_start: 0.7998 (tpp) cc_final: 0.7336 (tmm) REVERT: D 216 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7725 (mm) REVERT: D 272 LYS cc_start: 0.7745 (mtmm) cc_final: 0.7237 (mttt) REVERT: D 297 MET cc_start: 0.7936 (tmm) cc_final: 0.7099 (ttp) REVERT: D 387 PHE cc_start: 0.7802 (t80) cc_final: 0.5657 (m-80) REVERT: E 149 TYR cc_start: 0.8094 (m-80) cc_final: 0.7753 (m-80) REVERT: E 180 MET cc_start: 0.6607 (ttp) cc_final: 0.6325 (ttt) REVERT: E 183 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.5208 (m-80) REVERT: E 209 MET cc_start: 0.8824 (mpp) cc_final: 0.8565 (mpp) REVERT: E 328 TRP cc_start: 0.8677 (m100) cc_final: 0.8343 (m100) REVERT: F 175 GLU cc_start: 0.8008 (pp20) cc_final: 0.7542 (tp30) REVERT: F 190 PHE cc_start: 0.7103 (OUTLIER) cc_final: 0.6504 (t80) REVERT: F 241 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8000 (tp) REVERT: F 308 LEU cc_start: 0.7682 (mm) cc_final: 0.7464 (tp) outliers start: 84 outliers final: 56 residues processed: 374 average time/residue: 0.2262 time to fit residues: 126.9620 Evaluate side-chains 366 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 283 PHE Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 283 PHE Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 128 optimal weight: 0.0970 chunk 104 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13852 Z= 0.238 Angle : 0.623 13.264 18828 Z= 0.321 Chirality : 0.043 0.197 2052 Planarity : 0.004 0.049 2262 Dihedral : 12.571 161.138 1900 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.92 % Favored : 90.01 % Rotamer: Outliers : 6.50 % Allowed : 23.37 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1572 helix: 1.68 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.79 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 270 HIS 0.004 0.001 HIS D 224 PHE 0.027 0.001 PHE F 388 TYR 0.024 0.001 TYR C 362 ARG 0.003 0.000 ARG C 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 302 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.9110 (mt) cc_final: 0.8787 (mt) REVERT: A 366 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7784 (mp) REVERT: B 190 PHE cc_start: 0.7177 (t80) cc_final: 0.6922 (t80) REVERT: B 264 LYS cc_start: 0.7987 (tptt) cc_final: 0.7637 (mttp) REVERT: C 151 LYS cc_start: 0.8484 (mttt) cc_final: 0.8210 (mtmt) REVERT: C 154 LEU cc_start: 0.8296 (mm) cc_final: 0.8059 (tp) REVERT: C 180 MET cc_start: 0.2088 (mtt) cc_final: 0.1596 (mpp) REVERT: C 190 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6544 (t80) REVERT: C 236 MET cc_start: 0.7619 (mmm) cc_final: 0.7102 (mmm) REVERT: C 241 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 308 LEU cc_start: 0.7837 (mm) cc_final: 0.7558 (tp) REVERT: D 180 MET cc_start: 0.7985 (tpp) cc_final: 0.7163 (tmm) REVERT: D 197 ILE cc_start: 0.7491 (mm) cc_final: 0.7240 (tt) REVERT: D 216 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7831 (mm) REVERT: D 272 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7260 (mttt) REVERT: D 285 MET cc_start: 0.8003 (mmt) cc_final: 0.7411 (mmm) REVERT: D 296 TYR cc_start: 0.8186 (m-10) cc_final: 0.7122 (m-10) REVERT: D 297 MET cc_start: 0.7946 (tmm) cc_final: 0.7097 (ttp) REVERT: D 387 PHE cc_start: 0.7823 (t80) cc_final: 0.5640 (m-80) REVERT: E 180 MET cc_start: 0.6707 (ttp) cc_final: 0.6368 (ttt) REVERT: E 183 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.5104 (m-80) REVERT: E 191 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8790 (pp) REVERT: E 209 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8553 (mpp) REVERT: E 328 TRP cc_start: 0.8682 (m100) cc_final: 0.8406 (m100) REVERT: F 175 GLU cc_start: 0.8011 (pp20) cc_final: 0.7570 (tp30) REVERT: F 190 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6595 (t80) REVERT: F 236 MET cc_start: 0.7935 (mmm) cc_final: 0.7514 (mmm) REVERT: F 241 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8014 (tp) REVERT: F 308 LEU cc_start: 0.7742 (mm) cc_final: 0.7518 (tp) outliers start: 94 outliers final: 70 residues processed: 368 average time/residue: 0.2095 time to fit residues: 117.8163 Evaluate side-chains 363 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 284 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 375 SER Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 LEU Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 364 HIS Chi-restraints excluded: chain F residue 395 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.0470 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 321 ASN E 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13852 Z= 0.161 Angle : 0.584 10.614 18828 Z= 0.298 Chirality : 0.041 0.180 2052 Planarity : 0.004 0.046 2262 Dihedral : 12.350 161.126 1900 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.01 % Allowed : 26.90 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1572 helix: 1.93 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 320 HIS 0.005 0.001 HIS D 224 PHE 0.033 0.001 PHE F 388 TYR 0.023 0.001 TYR C 362 ARG 0.007 0.000 ARG F 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 293 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 PHE cc_start: 0.7138 (t80) cc_final: 0.6905 (t80) REVERT: B 264 LYS cc_start: 0.7985 (tptt) cc_final: 0.7691 (mttp) REVERT: C 151 LYS cc_start: 0.8413 (mttt) cc_final: 0.8210 (mtpt) REVERT: C 154 LEU cc_start: 0.8270 (mm) cc_final: 0.8041 (tp) REVERT: C 190 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6441 (t80) REVERT: C 241 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7891 (tp) REVERT: C 308 LEU cc_start: 0.7736 (mm) cc_final: 0.7308 (tt) REVERT: D 180 MET cc_start: 0.7924 (tpp) cc_final: 0.7390 (tmm) REVERT: D 197 ILE cc_start: 0.7463 (mm) cc_final: 0.7228 (tt) REVERT: D 216 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7800 (mm) REVERT: D 271 GLU cc_start: 0.7154 (mp0) cc_final: 0.6848 (mp0) REVERT: D 272 LYS cc_start: 0.7513 (mtmm) cc_final: 0.7263 (mttt) REVERT: D 296 TYR cc_start: 0.8327 (m-10) cc_final: 0.7258 (m-10) REVERT: D 297 MET cc_start: 0.7895 (tmm) cc_final: 0.7092 (ttp) REVERT: D 387 PHE cc_start: 0.7576 (t80) cc_final: 0.5520 (m-80) REVERT: E 180 MET cc_start: 0.6633 (ttp) cc_final: 0.6079 (ttt) REVERT: E 183 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4976 (m-80) REVERT: E 209 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8531 (mpp) REVERT: F 175 GLU cc_start: 0.8109 (pp20) cc_final: 0.7701 (tp30) REVERT: F 236 MET cc_start: 0.8061 (mmm) cc_final: 0.7835 (mmm) REVERT: F 241 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7955 (tp) REVERT: F 355 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8313 (tp) outliers start: 58 outliers final: 40 residues processed: 331 average time/residue: 0.2186 time to fit residues: 109.5280 Evaluate side-chains 326 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 279 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 0.0670 chunk 84 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 93 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN B 258 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13852 Z= 0.191 Angle : 0.594 9.852 18828 Z= 0.304 Chirality : 0.041 0.184 2052 Planarity : 0.004 0.045 2262 Dihedral : 12.279 160.707 1900 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.22 % Allowed : 26.76 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.22), residues: 1572 helix: 1.88 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 320 HIS 0.006 0.001 HIS D 344 PHE 0.026 0.001 PHE F 277 TYR 0.021 0.001 TYR C 362 ARG 0.002 0.000 ARG D 176 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7769 (mp) REVERT: B 190 PHE cc_start: 0.7062 (t80) cc_final: 0.6815 (t80) REVERT: B 264 LYS cc_start: 0.8208 (tptt) cc_final: 0.7780 (mttp) REVERT: C 151 LYS cc_start: 0.8473 (mttt) cc_final: 0.8063 (mtmt) REVERT: C 154 LEU cc_start: 0.8235 (mm) cc_final: 0.8001 (tp) REVERT: C 190 PHE cc_start: 0.7116 (OUTLIER) cc_final: 0.6497 (t80) REVERT: C 241 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7905 (tp) REVERT: D 180 MET cc_start: 0.7927 (tpp) cc_final: 0.7284 (tmm) REVERT: D 216 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7846 (mm) REVERT: D 296 TYR cc_start: 0.8363 (m-10) cc_final: 0.7264 (m-10) REVERT: D 297 MET cc_start: 0.7878 (tmm) cc_final: 0.7072 (ttp) REVERT: D 387 PHE cc_start: 0.7583 (t80) cc_final: 0.5523 (m-80) REVERT: E 180 MET cc_start: 0.6742 (ttp) cc_final: 0.6397 (ttt) REVERT: E 183 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.5023 (m-80) REVERT: E 209 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: E 328 TRP cc_start: 0.8671 (m100) cc_final: 0.8427 (m100) REVERT: E 342 HIS cc_start: 0.7388 (m170) cc_final: 0.7050 (m90) REVERT: E 343 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7865 (mt-10) REVERT: F 165 PHE cc_start: 0.8497 (t80) cc_final: 0.8295 (t80) REVERT: F 175 GLU cc_start: 0.8080 (pp20) cc_final: 0.7756 (tp30) REVERT: F 190 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6471 (t80) REVERT: F 241 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7913 (tp) REVERT: F 308 LEU cc_start: 0.7667 (tp) cc_final: 0.7349 (tt) REVERT: F 355 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8337 (tp) outliers start: 61 outliers final: 47 residues processed: 333 average time/residue: 0.2116 time to fit residues: 107.0377 Evaluate side-chains 336 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 280 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 268 SER Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 364 HIS Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 283 PHE Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN ** A 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13852 Z= 0.221 Angle : 0.624 14.521 18828 Z= 0.318 Chirality : 0.042 0.224 2052 Planarity : 0.004 0.058 2262 Dihedral : 12.298 162.515 1900 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 5.19 % Allowed : 26.49 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.22), residues: 1572 helix: 1.78 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 199 HIS 0.006 0.001 HIS C 222 PHE 0.026 0.001 PHE D 336 TYR 0.025 0.001 TYR C 362 ARG 0.002 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 281 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7795 (mp) REVERT: B 190 PHE cc_start: 0.7087 (t80) cc_final: 0.6816 (t80) REVERT: B 264 LYS cc_start: 0.8269 (tptt) cc_final: 0.7835 (mttp) REVERT: B 285 MET cc_start: 0.8437 (mtm) cc_final: 0.8210 (mtm) REVERT: C 151 LYS cc_start: 0.8498 (mttt) cc_final: 0.8084 (mtmt) REVERT: C 190 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6527 (t80) REVERT: C 241 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7824 (tp) REVERT: C 308 LEU cc_start: 0.7630 (tp) cc_final: 0.7136 (tt) REVERT: D 148 GLU cc_start: 0.8039 (tp30) cc_final: 0.7822 (tp30) REVERT: D 180 MET cc_start: 0.7891 (tpp) cc_final: 0.7196 (tmm) REVERT: D 203 MET cc_start: 0.7665 (pmm) cc_final: 0.6973 (mtt) REVERT: D 216 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7851 (mm) REVERT: D 296 TYR cc_start: 0.8442 (m-10) cc_final: 0.7307 (m-10) REVERT: D 297 MET cc_start: 0.7893 (tmm) cc_final: 0.7076 (ttp) REVERT: D 322 PHE cc_start: 0.8069 (p90) cc_final: 0.7737 (p90) REVERT: D 387 PHE cc_start: 0.7649 (t80) cc_final: 0.5556 (m-80) REVERT: E 183 TYR cc_start: 0.5806 (OUTLIER) cc_final: 0.5318 (m-80) REVERT: E 199 TRP cc_start: 0.6904 (p-90) cc_final: 0.6688 (p90) REVERT: E 209 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8555 (mpp) REVERT: E 296 TYR cc_start: 0.8307 (m-80) cc_final: 0.7431 (m-80) REVERT: E 342 HIS cc_start: 0.7395 (m170) cc_final: 0.7086 (m90) REVERT: E 343 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7823 (mt-10) REVERT: F 173 VAL cc_start: 0.8667 (t) cc_final: 0.8385 (p) REVERT: F 175 GLU cc_start: 0.8113 (pp20) cc_final: 0.7780 (tp30) REVERT: F 190 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6514 (t80) REVERT: F 236 MET cc_start: 0.7874 (mmm) cc_final: 0.7439 (mmm) REVERT: F 241 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7859 (tp) REVERT: F 308 LEU cc_start: 0.7830 (tp) cc_final: 0.7426 (tt) REVERT: F 355 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8336 (tp) REVERT: F 389 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7277 (mm-30) outliers start: 75 outliers final: 49 residues processed: 335 average time/residue: 0.2119 time to fit residues: 108.8174 Evaluate side-chains 329 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 271 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 364 HIS Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 258 HIS Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 190 PHE Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.0010 chunk 110 optimal weight: 4.9990 chunk 42 optimal weight: 0.2980 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS C 321 ASN D 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13852 Z= 0.177 Angle : 0.611 13.693 18828 Z= 0.309 Chirality : 0.041 0.255 2052 Planarity : 0.004 0.045 2262 Dihedral : 12.226 163.228 1900 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 4.01 % Allowed : 27.39 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1572 helix: 1.92 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.65 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 199 HIS 0.004 0.001 HIS F 174 PHE 0.030 0.001 PHE F 277 TYR 0.024 0.001 TYR C 362 ARG 0.002 0.000 ARG C 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 286 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7747 (mp) REVERT: B 190 PHE cc_start: 0.7054 (t80) cc_final: 0.6810 (t80) REVERT: B 264 LYS cc_start: 0.8213 (tptt) cc_final: 0.7837 (mttp) REVERT: B 285 MET cc_start: 0.8371 (mtm) cc_final: 0.8159 (mtm) REVERT: B 380 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7905 (mp) REVERT: C 151 LYS cc_start: 0.8449 (mttt) cc_final: 0.8010 (mtmt) REVERT: C 154 LEU cc_start: 0.8235 (mm) cc_final: 0.7965 (tp) REVERT: C 241 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7869 (tp) REVERT: C 308 LEU cc_start: 0.7633 (tp) cc_final: 0.7151 (tt) REVERT: D 155 SER cc_start: 0.7671 (m) cc_final: 0.6998 (t) REVERT: D 180 MET cc_start: 0.7802 (tpp) cc_final: 0.7371 (tmm) REVERT: D 203 MET cc_start: 0.7661 (pmm) cc_final: 0.6903 (mtt) REVERT: D 216 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7846 (mm) REVERT: D 296 TYR cc_start: 0.8384 (m-10) cc_final: 0.7280 (m-10) REVERT: D 297 MET cc_start: 0.7843 (tmm) cc_final: 0.7036 (ttp) REVERT: D 322 PHE cc_start: 0.8081 (p90) cc_final: 0.7780 (p90) REVERT: D 387 PHE cc_start: 0.7460 (t80) cc_final: 0.5509 (m-80) REVERT: E 148 GLU cc_start: 0.8184 (tp30) cc_final: 0.7858 (tp30) REVERT: E 180 MET cc_start: 0.6662 (ttt) cc_final: 0.6169 (ttt) REVERT: E 183 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: E 199 TRP cc_start: 0.7020 (p-90) cc_final: 0.6779 (p90) REVERT: E 209 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8558 (mpp) REVERT: E 342 HIS cc_start: 0.7247 (m170) cc_final: 0.6913 (m90) REVERT: E 343 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7822 (mt-10) REVERT: F 173 VAL cc_start: 0.8668 (t) cc_final: 0.8354 (p) REVERT: F 175 GLU cc_start: 0.8129 (pp20) cc_final: 0.7734 (tp30) REVERT: F 236 MET cc_start: 0.7949 (mmm) cc_final: 0.7366 (mmm) REVERT: F 241 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7834 (tp) REVERT: F 308 LEU cc_start: 0.7633 (tp) cc_final: 0.7317 (tt) REVERT: F 355 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8364 (tp) REVERT: F 380 ILE cc_start: 0.8180 (mm) cc_final: 0.7900 (mm) REVERT: F 389 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7137 (mm-30) outliers start: 58 outliers final: 45 residues processed: 326 average time/residue: 0.2089 time to fit residues: 104.8573 Evaluate side-chains 331 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 278 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 364 HIS Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 155 optimal weight: 0.0670 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13852 Z= 0.211 Angle : 0.641 14.238 18828 Z= 0.323 Chirality : 0.043 0.256 2052 Planarity : 0.004 0.045 2262 Dihedral : 12.197 163.662 1898 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.22 % Favored : 90.71 % Rotamer: Outliers : 3.94 % Allowed : 27.25 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.22), residues: 1572 helix: 1.79 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 320 HIS 0.013 0.001 HIS F 174 PHE 0.028 0.001 PHE D 336 TYR 0.024 0.001 TYR C 362 ARG 0.006 0.000 ARG E 318 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3144 Ramachandran restraints generated. 1572 Oldfield, 0 Emsley, 1572 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 284 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7738 (mp) REVERT: B 190 PHE cc_start: 0.7081 (t80) cc_final: 0.6838 (t80) REVERT: B 264 LYS cc_start: 0.8137 (tptt) cc_final: 0.7804 (mttp) REVERT: B 285 MET cc_start: 0.8401 (mtm) cc_final: 0.8194 (mtm) REVERT: C 151 LYS cc_start: 0.8500 (mttt) cc_final: 0.8050 (mtmt) REVERT: C 154 LEU cc_start: 0.8271 (mm) cc_final: 0.8011 (tp) REVERT: C 241 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7868 (tp) REVERT: C 308 LEU cc_start: 0.7633 (tp) cc_final: 0.7150 (tt) REVERT: D 180 MET cc_start: 0.7745 (tpp) cc_final: 0.7200 (tmm) REVERT: D 203 MET cc_start: 0.7640 (pmm) cc_final: 0.6987 (mtt) REVERT: D 216 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7837 (mm) REVERT: D 296 TYR cc_start: 0.8370 (m-10) cc_final: 0.7258 (m-10) REVERT: D 297 MET cc_start: 0.7946 (tmm) cc_final: 0.7120 (ttp) REVERT: D 322 PHE cc_start: 0.8024 (p90) cc_final: 0.7715 (p90) REVERT: D 387 PHE cc_start: 0.7547 (t80) cc_final: 0.5439 (m-80) REVERT: E 148 GLU cc_start: 0.8201 (tp30) cc_final: 0.7885 (tp30) REVERT: E 180 MET cc_start: 0.6800 (ttt) cc_final: 0.6474 (ttt) REVERT: E 183 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.5270 (m-80) REVERT: E 209 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8567 (mpp) REVERT: E 343 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7849 (mt-10) REVERT: F 173 VAL cc_start: 0.8696 (t) cc_final: 0.8405 (p) REVERT: F 175 GLU cc_start: 0.8052 (pp20) cc_final: 0.7734 (tp30) REVERT: F 241 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7809 (tp) REVERT: F 308 LEU cc_start: 0.7687 (tp) cc_final: 0.7365 (tt) REVERT: F 355 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8349 (tp) REVERT: F 380 ILE cc_start: 0.8183 (mm) cc_final: 0.7903 (mm) REVERT: F 389 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7260 (mm-30) outliers start: 57 outliers final: 46 residues processed: 327 average time/residue: 0.2145 time to fit residues: 107.8502 Evaluate side-chains 322 residues out of total 1446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 269 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 380 ILE Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 321 ASN Chi-restraints excluded: chain C residue 364 HIS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 364 HIS Chi-restraints excluded: chain D residue 382 PHE Chi-restraints excluded: chain D residue 395 THR Chi-restraints excluded: chain E residue 172 ILE Chi-restraints excluded: chain E residue 183 TYR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 209 MET Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 335 ILE Chi-restraints excluded: chain E residue 350 PHE Chi-restraints excluded: chain E residue 355 ILE Chi-restraints excluded: chain E residue 364 HIS Chi-restraints excluded: chain E residue 382 PHE Chi-restraints excluded: chain E residue 390 CYS Chi-restraints excluded: chain E residue 395 THR Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 241 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 364 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 108 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 ASN ** C 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.214303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160724 restraints weight = 16945.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.147531 restraints weight = 18886.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147529 restraints weight = 18687.901| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13852 Z= 0.190 Angle : 0.634 14.633 18828 Z= 0.320 Chirality : 0.042 0.250 2052 Planarity : 0.004 0.045 2262 Dihedral : 12.178 164.099 1898 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 3.94 % Allowed : 27.04 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1572 helix: 1.81 (0.17), residues: 912 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 320 HIS 0.012 0.001 HIS F 174 PHE 0.034 0.001 PHE D 201 TYR 0.024 0.001 TYR C 362 ARG 0.002 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.81 seconds wall clock time: 56 minutes 41.65 seconds (3401.65 seconds total)