Starting phenix.real_space_refine on Sun Mar 10 19:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n3c_0334/03_2024/6n3c_0334.pdb" } resolution = 3.3 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 2500 2.51 5 N 840 2.21 5 O 880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 293": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "C ARG 293": "NH1" <-> "NH2" Residue "D ARG 293": "NH1" <-> "NH2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "F ARG 293": "NH1" <-> "NH2" Residue "G ARG 293": "NH1" <-> "NH2" Residue "H ARG 293": "NH1" <-> "NH2" Residue "I ARG 293": "NH1" <-> "NH2" Residue "J ARG 293": "NH1" <-> "NH2" Residue "K ARG 293": "NH1" <-> "NH2" Residue "L ARG 293": "NH1" <-> "NH2" Residue "M ARG 293": "NH1" <-> "NH2" Residue "N ARG 293": "NH1" <-> "NH2" Residue "O ARG 293": "NH1" <-> "NH2" Residue "P ARG 293": "NH1" <-> "NH2" Residue "Q ARG 293": "NH1" <-> "NH2" Residue "R ARG 293": "NH1" <-> "NH2" Residue "S ARG 293": "NH1" <-> "NH2" Residue "T ARG 293": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4260 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "H" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "I" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "J" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "L" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "M" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "O" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "Q" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "S" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "T" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 213 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Time building chain proxies: 2.50, per 1000 atoms: 0.59 Number of scatterers: 4260 At special positions: 0 Unit cell: (86.92, 94.34, 47.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 880 8.00 N 840 7.00 C 2500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 960.1 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 292 through 293 removed outlier: 6.461A pdb=" N SER A 292 " --> pdb=" O ARG E 293 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 297 through 303 removed outlier: 8.822A pdb=" N ALA A 297 " --> pdb=" O GLY E 298 " (cutoff:3.500A) removed outlier: 10.331A pdb=" N GLY E 300 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU A 299 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASN E 302 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN A 301 " --> pdb=" O ASN E 302 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY A 298 " --> pdb=" O ALA K 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU K 299 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 300 " --> pdb=" O LEU K 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY K 298 " --> pdb=" O ALA O 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU O 299 " --> pdb=" O GLY K 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY K 300 " --> pdb=" O LEU O 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY O 298 " --> pdb=" O ALA S 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU S 299 " --> pdb=" O GLY O 298 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY O 300 " --> pdb=" O LEU S 299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 306 through 308 removed outlier: 6.125A pdb=" N ASN A 306 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 311 through 318 removed outlier: 5.950A pdb=" N ASN A 312 " --> pdb=" O PHE E 313 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLU E 315 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLY A 314 " --> pdb=" O GLU E 315 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N SER E 317 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N PHE A 316 " --> pdb=" O SER E 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 292 through 293 removed outlier: 6.563A pdb=" N SER B 292 " --> pdb=" O ARG F 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 312 through 314 removed outlier: 6.179A pdb=" N PHE B 313 " --> pdb=" O GLY L 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE L 313 " --> pdb=" O GLY P 314 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE P 313 " --> pdb=" O GLY T 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AA8, first strand: chain 'C' and resid 297 through 303 removed outlier: 6.833A pdb=" N GLY C 298 " --> pdb=" O ALA G 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU G 299 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY C 300 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY G 298 " --> pdb=" O ALA I 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU I 299 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY G 300 " --> pdb=" O LEU I 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 298 " --> pdb=" O ALA M 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU M 299 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY I 300 " --> pdb=" O LEU M 299 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY M 298 " --> pdb=" O ALA Q 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU Q 299 " --> pdb=" O GLY M 298 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY M 300 " --> pdb=" O LEU Q 299 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 311 through 318 Processing sheet with id=AB2, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AB3, first strand: chain 'D' and resid 312 through 314 removed outlier: 6.180A pdb=" N PHE D 313 " --> pdb=" O GLY H 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE H 313 " --> pdb=" O GLY J 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE J 313 " --> pdb=" O GLY N 314 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE N 313 " --> pdb=" O GLY R 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 100 hydrogen bonds defined for protein. 300 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: 0.99 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1606 1.34 - 1.45: 742 1.45 - 1.57: 1872 1.57 - 1.68: 0 1.68 - 1.80: 80 Bond restraints: 4300 Sorted by residual: bond pdb=" N GLN S 303 " pdb=" CA GLN S 303 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.62e+00 bond pdb=" N GLN E 303 " pdb=" CA GLN E 303 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.54e+00 bond pdb=" N PHE C 289 " pdb=" CA PHE C 289 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.45e+00 bond pdb=" N PHE I 289 " pdb=" CA PHE I 289 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.40e+00 bond pdb=" N GLN G 303 " pdb=" CA GLN G 303 " ideal model delta sigma weight residual 1.457 1.490 -0.034 1.24e-02 6.50e+03 7.39e+00 ... (remaining 4295 not shown) Histogram of bond angle deviations from ideal: 99.79 - 105.08: 94 105.08 - 110.38: 658 110.38 - 115.68: 1428 115.68 - 120.97: 2072 120.97 - 126.27: 1388 Bond angle restraints: 5640 Sorted by residual: angle pdb=" N GLY D 294 " pdb=" CA GLY D 294 " pdb=" C GLY D 294 " ideal model delta sigma weight residual 112.82 107.51 5.31 1.38e+00 5.25e-01 1.48e+01 angle pdb=" N GLY P 294 " pdb=" CA GLY P 294 " pdb=" C GLY P 294 " ideal model delta sigma weight residual 112.82 107.52 5.30 1.38e+00 5.25e-01 1.47e+01 angle pdb=" N GLY F 294 " pdb=" CA GLY F 294 " pdb=" C GLY F 294 " ideal model delta sigma weight residual 112.82 107.54 5.28 1.38e+00 5.25e-01 1.47e+01 angle pdb=" N GLY T 294 " pdb=" CA GLY T 294 " pdb=" C GLY T 294 " ideal model delta sigma weight residual 112.82 107.55 5.27 1.38e+00 5.25e-01 1.46e+01 angle pdb=" N GLY B 294 " pdb=" CA GLY B 294 " pdb=" C GLY B 294 " ideal model delta sigma weight residual 112.82 107.56 5.26 1.38e+00 5.25e-01 1.46e+01 ... (remaining 5635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.42: 1860 12.42 - 24.84: 250 24.84 - 37.25: 130 37.25 - 49.67: 0 49.67 - 62.09: 20 Dihedral angle restraints: 2260 sinusoidal: 840 harmonic: 1420 Sorted by residual: dihedral pdb=" CA ASN B 312 " pdb=" C ASN B 312 " pdb=" N PHE B 313 " pdb=" CA PHE B 313 " ideal model delta harmonic sigma weight residual 180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN P 312 " pdb=" C ASN P 312 " pdb=" N PHE P 313 " pdb=" CA PHE P 313 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASN D 312 " pdb=" C ASN D 312 " pdb=" N PHE D 313 " pdb=" CA PHE D 313 " ideal model delta harmonic sigma weight residual -180.00 -162.69 -17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 2257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 310 0.050 - 0.100: 60 0.100 - 0.150: 47 0.150 - 0.200: 13 0.200 - 0.250: 10 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA SER M 305 " pdb=" N SER M 305 " pdb=" C SER M 305 " pdb=" CB SER M 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA SER E 305 " pdb=" N SER E 305 " pdb=" C SER E 305 " pdb=" CB SER E 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA SER I 305 " pdb=" N SER I 305 " pdb=" C SER I 305 " pdb=" CB SER I 305 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 437 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY O 304 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.18e+00 pdb=" C GLY O 304 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY O 304 " -0.013 2.00e-02 2.50e+03 pdb=" N SER O 305 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 304 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C GLY G 304 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY G 304 " 0.013 2.00e-02 2.50e+03 pdb=" N SER G 305 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 304 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C GLY M 304 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY M 304 " 0.013 2.00e-02 2.50e+03 pdb=" N SER M 305 " 0.012 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1842 2.89 - 3.39: 3758 3.39 - 3.89: 7085 3.89 - 4.40: 8792 4.40 - 4.90: 17058 Nonbonded interactions: 38535 Sorted by model distance: nonbonded pdb=" ND2 ASN A 302 " pdb=" OG SER A 305 " model vdw 2.387 2.520 nonbonded pdb=" ND2 ASN C 302 " pdb=" OG SER C 305 " model vdw 2.387 2.520 nonbonded pdb=" ND2 ASN K 302 " pdb=" OG SER K 305 " model vdw 2.388 2.520 nonbonded pdb=" ND2 ASN I 302 " pdb=" OG SER I 305 " model vdw 2.388 2.520 nonbonded pdb=" ND2 ASN S 302 " pdb=" OG SER S 305 " model vdw 2.388 2.520 ... (remaining 38530 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.090 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: 0.700 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.130 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 : 0.009 0.035 4300 Z= 0.624 Angle : 1.311 8.550 5640 Z= 0.786 Chirality : 0.073 0.250 440 Planarity : 0.004 0.020 860 Dihedral : 14.000 62.088 1460 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % 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: -5.01 (0.17), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.13), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE M 313 ARG 0.001 0.000 ARG N 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.442 Fit side-chains REVERT: C 291 ASN cc_start: 0.8565 (p0) cc_final: 0.7128 (m-40) REVERT: C 305 SER cc_start: 0.7761 (p) cc_final: 0.7471 (m) REVERT: C 315 GLU cc_start: 0.8507 (tt0) cc_final: 0.8251 (tt0) REVERT: E 311 MET cc_start: 0.8956 (ttt) cc_final: 0.8665 (ttm) REVERT: F 307 MET cc_start: 0.7926 (mmt) cc_final: 0.7668 (mmt) REVERT: G 311 MET cc_start: 0.8909 (ttt) cc_final: 0.8596 (ttm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.1077 time to fit residues: 12.9159 Evaluate side-chains 70 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.0670 chunk 45 optimal weight: 30.0000 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 overall best weight: 6.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 302 ASN I 302 ASN K 302 ASN M 302 ASN O 302 ASN Q 302 ASN S 302 ASN T 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4300 Z= 0.293 Angle : 0.588 8.017 5640 Z= 0.294 Chirality : 0.044 0.130 440 Planarity : 0.002 0.011 860 Dihedral : 5.609 16.688 640 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 6.58 % Allowed : 22.37 % Favored : 71.05 % 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: -4.49 (0.21), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.16), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE G 313 ARG 0.001 0.000 ARG S 293 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: C 291 ASN cc_start: 0.8853 (p0) cc_final: 0.7046 (m-40) REVERT: C 315 GLU cc_start: 0.8421 (tt0) cc_final: 0.8163 (tt0) REVERT: G 311 MET cc_start: 0.8863 (ttt) cc_final: 0.8645 (ttm) outliers start: 25 outliers final: 20 residues processed: 88 average time/residue: 0.1010 time to fit residues: 12.3642 Evaluate side-chains 89 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 40.0000 chunk 16 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 37 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 18 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.056 4300 Z= 0.779 Angle : 0.839 10.065 5640 Z= 0.425 Chirality : 0.050 0.163 440 Planarity : 0.004 0.025 860 Dihedral : 6.583 20.416 640 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 10.53 % Allowed : 24.74 % Favored : 64.74 % 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: -4.53 (0.20), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.15), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.025 0.003 PHE O 313 ARG 0.003 0.001 ARG S 293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 67 time to evaluate : 0.476 Fit side-chains REVERT: C 315 GLU cc_start: 0.8409 (tt0) cc_final: 0.8200 (tt0) REVERT: J 291 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8887 (p0) REVERT: P 307 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7360 (ttm) REVERT: Q 303 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7461 (mt0) REVERT: S 303 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.7472 (mt0) outliers start: 40 outliers final: 32 residues processed: 93 average time/residue: 0.1049 time to fit residues: 13.5509 Evaluate side-chains 101 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 65 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 291 ASN Chi-restraints excluded: chain J residue 306 ASN Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 292 SER Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain P residue 292 SER Chi-restraints excluded: chain P residue 306 ASN Chi-restraints excluded: chain P residue 307 MET Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN J 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4300 Z= 0.336 Angle : 0.615 8.490 5640 Z= 0.306 Chirality : 0.042 0.141 440 Planarity : 0.002 0.012 860 Dihedral : 5.750 17.618 640 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 10.79 % Allowed : 24.21 % Favored : 65.00 % 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: -4.18 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.002 PHE G 313 ARG 0.001 0.000 ARG Q 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 82 time to evaluate : 0.464 Fit side-chains REVERT: C 315 GLU cc_start: 0.8356 (tt0) cc_final: 0.8125 (tt0) REVERT: D 307 MET cc_start: 0.8119 (ttm) cc_final: 0.7883 (ttm) REVERT: G 311 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8074 (ttt) outliers start: 41 outliers final: 27 residues processed: 100 average time/residue: 0.1033 time to fit residues: 14.4060 Evaluate side-chains 104 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 306 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 30.0000 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4300 Z= 0.274 Angle : 0.567 8.372 5640 Z= 0.283 Chirality : 0.041 0.157 440 Planarity : 0.002 0.009 860 Dihedral : 5.478 17.371 640 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 11.32 % Allowed : 23.95 % Favored : 64.74 % 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: -3.93 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE G 313 ARG 0.001 0.000 ARG Q 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 77 time to evaluate : 0.442 Fit side-chains REVERT: C 315 GLU cc_start: 0.8317 (tt0) cc_final: 0.8092 (tt0) REVERT: G 311 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8241 (ttm) REVERT: Q 303 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.7304 (mt0) REVERT: T 307 MET cc_start: 0.8169 (mtt) cc_final: 0.7790 (ttm) outliers start: 43 outliers final: 29 residues processed: 96 average time/residue: 0.1065 time to fit residues: 14.4165 Evaluate side-chains 105 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 74 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 311 MET Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 48 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.051 4300 Z= 0.704 Angle : 0.781 9.474 5640 Z= 0.398 Chirality : 0.047 0.157 440 Planarity : 0.003 0.023 860 Dihedral : 6.295 18.947 640 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.67 % Favored : 84.33 % Rotamer: Outliers : 11.58 % Allowed : 23.42 % Favored : 65.00 % 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: -4.31 (0.22), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.17), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.002 PHE O 313 ARG 0.002 0.000 ARG S 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 69 time to evaluate : 0.480 Fit side-chains REVERT: C 315 GLU cc_start: 0.8361 (tt0) cc_final: 0.8159 (tt0) REVERT: Q 303 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: S 303 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7326 (mt0) outliers start: 44 outliers final: 36 residues processed: 93 average time/residue: 0.1099 time to fit residues: 14.1920 Evaluate side-chains 105 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 67 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain B residue 307 MET Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 307 MET Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 311 MET Chi-restraints excluded: chain S residue 318 ILE Chi-restraints excluded: chain T residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 57 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4300 Z= 0.276 Angle : 0.576 8.284 5640 Z= 0.288 Chirality : 0.041 0.151 440 Planarity : 0.002 0.008 860 Dihedral : 5.610 18.056 640 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 10.79 % Allowed : 24.21 % Favored : 65.00 % 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: -4.03 (0.25), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.002 PHE G 313 ARG 0.001 0.000 ARG Q 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 79 time to evaluate : 0.437 Fit side-chains REVERT: C 315 GLU cc_start: 0.8310 (tt0) cc_final: 0.8082 (tt0) REVERT: G 311 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8434 (ttm) REVERT: L 306 ASN cc_start: 0.8788 (m-40) cc_final: 0.8581 (m-40) REVERT: Q 303 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.7344 (mt0) outliers start: 41 outliers final: 33 residues processed: 97 average time/residue: 0.1062 time to fit residues: 14.5430 Evaluate side-chains 112 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 77 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 311 MET Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain H residue 291 ASN Chi-restraints excluded: chain H residue 306 ASN Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 overall best weight: 13.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 4300 Z= 0.569 Angle : 0.729 9.675 5640 Z= 0.364 Chirality : 0.045 0.151 440 Planarity : 0.003 0.017 860 Dihedral : 6.055 18.927 640 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 11.05 % Allowed : 25.00 % Favored : 63.95 % 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: -4.17 (0.23), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.17 (0.18), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.002 PHE O 313 ARG 0.002 0.000 ARG S 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 72 time to evaluate : 0.507 Fit side-chains REVERT: C 315 GLU cc_start: 0.8324 (tt0) cc_final: 0.8121 (tt0) REVERT: L 307 MET cc_start: 0.8109 (tpp) cc_final: 0.7832 (ttm) REVERT: Q 303 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: R 307 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: S 303 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7362 (mt0) outliers start: 42 outliers final: 35 residues processed: 92 average time/residue: 0.1058 time to fit residues: 13.5533 Evaluate side-chains 108 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 70 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain J residue 311 MET Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain Q residue 303 GLN Chi-restraints excluded: chain R residue 307 MET Chi-restraints excluded: chain R residue 311 MET Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 303 GLN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4300 Z= 0.242 Angle : 0.567 8.533 5640 Z= 0.282 Chirality : 0.041 0.149 440 Planarity : 0.002 0.008 860 Dihedral : 5.449 20.144 640 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 9.74 % Allowed : 25.53 % Favored : 64.74 % 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: -3.83 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE G 313 ARG 0.002 0.000 ARG Q 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 0.491 Fit side-chains REVERT: C 315 GLU cc_start: 0.8309 (tt0) cc_final: 0.8057 (tt0) REVERT: I 311 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8234 (ttt) REVERT: J 307 MET cc_start: 0.8020 (tpp) cc_final: 0.7277 (tpt) REVERT: N 311 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7595 (ttp) outliers start: 37 outliers final: 30 residues processed: 93 average time/residue: 0.1072 time to fit residues: 14.0322 Evaluate side-chains 109 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 77 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 311 MET Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 11.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4300 Z= 0.476 Angle : 0.673 8.816 5640 Z= 0.339 Chirality : 0.044 0.152 440 Planarity : 0.002 0.015 860 Dihedral : 5.859 17.667 640 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 9.74 % Allowed : 25.00 % Favored : 65.26 % 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: -3.95 (0.24), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.021 0.002 PHE Q 313 ARG 0.002 0.000 ARG Q 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 74 time to evaluate : 0.521 Fit side-chains REVERT: C 315 GLU cc_start: 0.8342 (tt0) cc_final: 0.8122 (tt0) outliers start: 37 outliers final: 33 residues processed: 92 average time/residue: 0.1072 time to fit residues: 14.0926 Evaluate side-chains 107 residues out of total 380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 74 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ASN Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 291 ASN Chi-restraints excluded: chain C residue 291 ASN Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain D residue 291 ASN Chi-restraints excluded: chain E residue 291 ASN Chi-restraints excluded: chain E residue 305 SER Chi-restraints excluded: chain E residue 311 MET Chi-restraints excluded: chain G residue 291 ASN Chi-restraints excluded: chain G residue 305 SER Chi-restraints excluded: chain G residue 318 ILE Chi-restraints excluded: chain I residue 291 ASN Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain I residue 311 MET Chi-restraints excluded: chain K residue 291 ASN Chi-restraints excluded: chain K residue 305 SER Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain L residue 318 ILE Chi-restraints excluded: chain M residue 291 ASN Chi-restraints excluded: chain M residue 305 SER Chi-restraints excluded: chain M residue 318 ILE Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 291 ASN Chi-restraints excluded: chain O residue 305 SER Chi-restraints excluded: chain O residue 318 ILE Chi-restraints excluded: chain P residue 291 ASN Chi-restraints excluded: chain P residue 311 MET Chi-restraints excluded: chain Q residue 291 ASN Chi-restraints excluded: chain S residue 291 ASN Chi-restraints excluded: chain S residue 305 SER Chi-restraints excluded: chain S residue 318 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.157813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.142730 restraints weight = 6199.632| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.05 r_work: 0.4173 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.4071 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4300 Z= 0.231 Angle : 0.583 9.082 5640 Z= 0.289 Chirality : 0.040 0.149 440 Planarity : 0.001 0.008 860 Dihedral : 5.458 19.445 640 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 10.00 % Allowed : 23.95 % Favored : 66.05 % 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: -3.80 (0.26), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.20), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE G 313 ARG 0.002 0.000 ARG Q 293 =============================================================================== Job complete usr+sys time: 981.79 seconds wall clock time: 18 minutes 39.70 seconds (1119.70 seconds total)