Starting phenix.real_space_refine on Tue Feb 13 22:46:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ukc_26576/02_2024/7ukc_26576.pdb" } resolution = 3.0 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= 0.005 sd= 0.060 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 K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "C PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.01, per 1000 atoms: 0.63 Number of scatterers: 8000 At special positions: 0 Unit cell: (108.206, 106.554, 83.426, 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) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.6 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 220 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 321 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 424 Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 181 through 205 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR C 225 " --> pdb=" O CYS C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 278 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 298 through 307 removed outlier: 3.802A pdb=" N LYS C 302 " --> pdb=" O PHE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER C 322 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLU C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 Processing helix chain 'C' and resid 400 through 423 removed outlier: 4.419A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 220 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 280 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.507A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 320 Processing helix chain 'D' and resid 321 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 400 removed outlier: 3.640A pdb=" N LEU D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 424 Processing helix chain 'A' and resid 167 through 177 Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 181 through 205 Processing helix chain 'A' and resid 220 through 225 removed outlier: 3.538A pdb=" N TYR A 225 " --> pdb=" O CYS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.803A pdb=" N LYS A 302 " --> pdb=" O PHE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 347 removed outlier: 5.359A pdb=" N SER A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLU A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.844A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 400 Processing helix chain 'A' and resid 400 through 423 removed outlier: 4.420A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1815 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 1525 1.46 - 1.57: 4139 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CB GLU C 346 " pdb=" CG GLU C 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CB GLU A 346 " pdb=" CG GLU A 346 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG GLU A 346 " pdb=" CD GLU A 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CG GLU C 346 " pdb=" CD GLU C 346 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB LEU D 371 " pdb=" CG LEU D 371 " ideal model delta sigma weight residual 1.530 1.504 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.61: 150 105.61 - 112.74: 4399 112.74 - 119.87: 2674 119.87 - 127.00: 3833 127.00 - 134.12: 68 Bond angle restraints: 11124 Sorted by residual: angle pdb=" C PHE A 175 " pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.70e+01 angle pdb=" C PHE C 175 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 122.38 114.93 7.45 1.81e+00 3.05e-01 1.69e+01 angle pdb=" C ILE B 270 " pdb=" CA ILE B 270 " pdb=" CB ILE B 270 " ideal model delta sigma weight residual 111.65 107.18 4.47 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C ILE D 270 " pdb=" CA ILE D 270 " pdb=" CB ILE D 270 " ideal model delta sigma weight residual 111.65 107.20 4.45 1.41e+00 5.03e-01 9.98e+00 angle pdb=" N GLU A 176 " pdb=" CA GLU A 176 " pdb=" CB GLU A 176 " ideal model delta sigma weight residual 110.44 114.14 -3.70 1.53e+00 4.27e-01 5.84e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 4334 16.23 - 32.46: 376 32.46 - 48.69: 72 48.69 - 64.93: 6 64.93 - 81.16: 4 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ARG C 293 " pdb=" C ARG C 293 " pdb=" N VAL C 294 " pdb=" CA VAL C 294 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG A 293 " pdb=" C ARG A 293 " pdb=" N VAL A 294 " pdb=" CA VAL A 294 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA THR A 370 " pdb=" C THR A 370 " pdb=" N LEU A 371 " pdb=" CA LEU A 371 " ideal model delta harmonic sigma weight residual 180.00 163.69 16.31 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 793 0.035 - 0.070: 388 0.070 - 0.106: 92 0.106 - 0.141: 43 0.141 - 0.176: 4 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA GLU B 176 " pdb=" N GLU B 176 " pdb=" C GLU B 176 " pdb=" CB GLU B 176 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA GLU D 176 " pdb=" N GLU D 176 " pdb=" C GLU D 176 " pdb=" CB GLU D 176 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA PHE C 194 " pdb=" N PHE C 194 " pdb=" C PHE C 194 " pdb=" CB PHE C 194 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 172 " 0.020 2.00e-02 2.50e+03 1.61e-02 6.51e+00 pdb=" CG TRP B 172 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 172 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 172 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 172 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 172 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 172 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 172 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 172 " -0.020 2.00e-02 2.50e+03 1.61e-02 6.47e+00 pdb=" CG TRP D 172 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP D 172 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 172 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 172 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 172 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 172 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 172 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 172 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 346 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CD GLU D 346 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU D 346 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU D 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 661 2.73 - 3.33: 10452 3.33 - 3.93: 15425 3.93 - 4.54: 21774 4.54 - 5.14: 32004 Nonbonded interactions: 80316 Sorted by model distance: nonbonded pdb=" OH TYR C 188 " pdb=" O HIS C 306 " model vdw 2.127 2.440 nonbonded pdb=" OH TYR A 188 " pdb=" O HIS A 306 " model vdw 2.128 2.440 nonbonded pdb=" OE2 GLU D 205 " pdb=" NH2 ARG D 293 " model vdw 2.282 2.520 nonbonded pdb=" OE2 GLU B 205 " pdb=" NH2 ARG B 293 " model vdw 2.283 2.520 nonbonded pdb=" OG1 THR D 367 " pdb=" OH TYR A 373 " model vdw 2.307 2.440 ... (remaining 80311 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 166 through 424) selection = (chain 'B' and resid 166 through 424) selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.000 Extract box with map and model: 12.210 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.200 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8188 Z= 0.359 Angle : 0.670 8.420 11124 Z= 0.385 Chirality : 0.045 0.176 1320 Planarity : 0.004 0.037 1360 Dihedral : 12.536 81.157 2840 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 0.00 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.26), residues: 1028 helix: 0.61 (0.18), residues: 812 sheet: None (None), residues: 0 loop : -0.42 (0.47), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP B 172 HIS 0.006 0.001 HIS A 306 PHE 0.017 0.002 PHE C 175 TYR 0.015 0.002 TYR B 188 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.805 Fit side-chains REVERT: D 187 PHE cc_start: 0.7783 (t80) cc_final: 0.7431 (t80) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 1.1367 time to fit residues: 172.5940 Evaluate side-chains 117 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 116 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 177 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8188 Z= 0.243 Angle : 0.547 7.646 11124 Z= 0.293 Chirality : 0.041 0.142 1320 Planarity : 0.005 0.042 1360 Dihedral : 4.223 23.103 1150 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.78 % Allowed : 11.26 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1028 helix: 1.12 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -0.22 (0.48), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 172 HIS 0.002 0.001 HIS C 306 PHE 0.015 0.001 PHE A 257 TYR 0.015 0.001 TYR D 188 ARG 0.004 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.083 Fit side-chains REVERT: A 422 ARG cc_start: 0.5410 (ptm160) cc_final: 0.5195 (ptm-80) outliers start: 15 outliers final: 4 residues processed: 134 average time/residue: 1.1537 time to fit residues: 164.3695 Evaluate side-chains 124 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 177 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8188 Z= 0.368 Angle : 0.573 7.153 11124 Z= 0.306 Chirality : 0.043 0.190 1320 Planarity : 0.005 0.045 1360 Dihedral : 4.137 19.085 1148 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.13 % Allowed : 13.74 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.26), residues: 1028 helix: 1.07 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.28 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 172 HIS 0.003 0.001 HIS B 306 PHE 0.016 0.001 PHE A 257 TYR 0.015 0.001 TYR D 188 ARG 0.003 0.000 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.883 Fit side-chains REVERT: B 264 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8460 (mt) REVERT: A 170 ARG cc_start: 0.7099 (tmt170) cc_final: 0.6879 (tmt170) REVERT: A 422 ARG cc_start: 0.5511 (ptm160) cc_final: 0.5272 (ptm-80) outliers start: 18 outliers final: 8 residues processed: 134 average time/residue: 1.2439 time to fit residues: 176.2941 Evaluate side-chains 127 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 118 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.2980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 408 ASN C 408 ASN D 177 ASN D 408 ASN A 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8188 Z= 0.191 Angle : 0.506 6.784 11124 Z= 0.272 Chirality : 0.039 0.170 1320 Planarity : 0.005 0.047 1360 Dihedral : 3.886 19.054 1148 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.78 % Allowed : 16.11 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1028 helix: 1.36 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -0.03 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 172 HIS 0.002 0.001 HIS C 179 PHE 0.022 0.001 PHE C 257 TYR 0.015 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.899 Fit side-chains REVERT: A 422 ARG cc_start: 0.5471 (ptm160) cc_final: 0.5271 (ptm-80) outliers start: 15 outliers final: 6 residues processed: 132 average time/residue: 1.2399 time to fit residues: 173.5649 Evaluate side-chains 127 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 121 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 408 ASN C 408 ASN D 177 ASN D 408 ASN A 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8188 Z= 0.377 Angle : 0.572 6.656 11124 Z= 0.306 Chirality : 0.043 0.153 1320 Planarity : 0.005 0.044 1360 Dihedral : 3.990 17.455 1148 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.01 % Allowed : 18.13 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.26), residues: 1028 helix: 1.24 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -0.09 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 362 HIS 0.002 0.001 HIS B 306 PHE 0.023 0.002 PHE A 257 TYR 0.015 0.001 TYR D 188 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 121 time to evaluate : 0.896 Fit side-chains REVERT: A 183 MET cc_start: 0.5462 (ppp) cc_final: 0.5242 (ppp) REVERT: A 318 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.5124 (tppt) REVERT: A 422 ARG cc_start: 0.5551 (ptm160) cc_final: 0.5331 (ptm-80) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 1.1791 time to fit residues: 162.5194 Evaluate side-chains 127 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 117 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8188 Z= 0.220 Angle : 0.510 6.421 11124 Z= 0.273 Chirality : 0.040 0.130 1320 Planarity : 0.005 0.046 1360 Dihedral : 3.854 17.581 1148 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.01 % Allowed : 18.72 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1028 helix: 1.43 (0.18), residues: 820 sheet: None (None), residues: 0 loop : -0.01 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 172 HIS 0.002 0.000 HIS B 306 PHE 0.026 0.001 PHE C 257 TYR 0.013 0.001 TYR D 188 ARG 0.003 0.000 ARG B 247 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.892 Fit side-chains REVERT: C 318 LYS cc_start: 0.7105 (OUTLIER) cc_final: 0.5182 (tppt) REVERT: A 422 ARG cc_start: 0.5379 (ptm160) cc_final: 0.5015 (ptm-80) outliers start: 17 outliers final: 10 residues processed: 126 average time/residue: 1.2637 time to fit residues: 168.3670 Evaluate side-chains 127 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 116 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 415 GLN Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0070 chunk 70 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 408 ASN C 408 ASN D 177 ASN D 408 ASN A 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8188 Z= 0.168 Angle : 0.486 6.266 11124 Z= 0.258 Chirality : 0.039 0.140 1320 Planarity : 0.005 0.045 1360 Dihedral : 3.705 17.633 1148 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.25 % Allowed : 19.79 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.27), residues: 1028 helix: 1.68 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.15 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 172 HIS 0.001 0.000 HIS B 306 PHE 0.030 0.001 PHE A 257 TYR 0.013 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.824 Fit side-chains outliers start: 19 outliers final: 8 residues processed: 139 average time/residue: 1.1805 time to fit residues: 173.9438 Evaluate side-chains 128 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 333 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.0770 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN B 408 ASN C 408 ASN D 177 ASN D 408 ASN A 408 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.198 Angle : 0.511 6.852 11124 Z= 0.271 Chirality : 0.039 0.157 1320 Planarity : 0.004 0.043 1360 Dihedral : 3.679 18.170 1148 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.66 % Allowed : 20.97 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1028 helix: 1.66 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.03 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.039 0.001 PHE A 257 TYR 0.012 0.001 TYR D 188 ARG 0.003 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 124 time to evaluate : 0.877 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 132 average time/residue: 1.1767 time to fit residues: 165.4298 Evaluate side-chains 126 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 177 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.226 Angle : 0.526 7.578 11124 Z= 0.278 Chirality : 0.040 0.149 1320 Planarity : 0.004 0.041 1360 Dihedral : 3.685 18.893 1148 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.42 % Allowed : 21.68 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1028 helix: 1.64 (0.18), residues: 818 sheet: None (None), residues: 0 loop : 0.01 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.036 0.001 PHE A 257 TYR 0.012 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.921 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 1.3212 time to fit residues: 185.9494 Evaluate side-chains 132 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN C 408 ASN D 177 ASN A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8188 Z= 0.206 Angle : 0.533 8.456 11124 Z= 0.282 Chirality : 0.040 0.143 1320 Planarity : 0.004 0.041 1360 Dihedral : 3.664 19.336 1148 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.42 % Allowed : 21.92 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1028 helix: 1.71 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.11 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 172 HIS 0.002 0.000 HIS D 306 PHE 0.040 0.001 PHE C 257 TYR 0.012 0.001 TYR B 188 ARG 0.002 0.000 ARG D 247 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: C 262 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6408 (mmp) outliers start: 12 outliers final: 8 residues processed: 131 average time/residue: 1.2815 time to fit residues: 177.3833 Evaluate side-chains 130 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 323 GLU Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0870 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 177 ASN ** B 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 ASN D 177 ASN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.179503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.130464 restraints weight = 9383.551| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.60 r_work: 0.3220 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8188 Z= 0.223 Angle : 0.545 9.225 11124 Z= 0.287 Chirality : 0.040 0.143 1320 Planarity : 0.004 0.040 1360 Dihedral : 3.672 17.129 1148 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.66 % Allowed : 21.92 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.26), residues: 1028 helix: 1.69 (0.18), residues: 810 sheet: None (None), residues: 0 loop : 0.06 (0.46), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 172 HIS 0.002 0.000 HIS B 306 PHE 0.045 0.001 PHE C 257 TYR 0.012 0.001 TYR D 188 ARG 0.002 0.000 ARG D 247 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3368.31 seconds wall clock time: 60 minutes 46.24 seconds (3646.24 seconds total)