Starting phenix.real_space_refine on Mon Mar 18 08:59:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5gaq_8015/03_2024/5gaq_8015.pdb" } resolution = 3.1 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= 0.001 sd= 0.009 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 72 5.16 5 C 13032 2.51 5 N 3465 2.21 5 O 4005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "H TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 294": "OE1" <-> "OE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 294": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20574 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2286 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 278} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 11.15, per 1000 atoms: 0.54 Number of scatterers: 20574 At special positions: 0 Unit cell: (132.99, 134.42, 114.4, 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 72 16.00 O 4005 8.00 N 3465 7.00 C 13032 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: 7.62 Conformation dependent library (CDL) restraints added in 3.6 seconds 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4770 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 0 sheets defined 1.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.513A pdb=" N GLN B 243 " --> pdb=" O ASN B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'C' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN C 243 " --> pdb=" O ASN C 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'D' and resid 240 through 243 removed outlier: 3.507A pdb=" N GLN D 243 " --> pdb=" O ASN D 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 243' Processing helix chain 'E' and resid 240 through 243 removed outlier: 3.509A pdb=" N GLN E 243 " --> pdb=" O ASN E 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 240 through 243' Processing helix chain 'F' and resid 240 through 243 removed outlier: 3.515A pdb=" N GLN F 243 " --> pdb=" O ASN F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 240 through 243' Processing helix chain 'G' and resid 240 through 243 removed outlier: 3.511A pdb=" N GLN G 243 " --> pdb=" O ASN G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 240 through 243' Processing helix chain 'H' and resid 240 through 243 removed outlier: 3.506A pdb=" N GLN H 243 " --> pdb=" O ASN H 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 240 through 243' Processing helix chain 'I' and resid 240 through 243 removed outlier: 3.508A pdb=" N GLN I 243 " --> pdb=" O ASN I 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 240 through 243' No hydrogen bonds 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: 0.06 Time building geometry restraints manager: 8.29 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: 6513 1.34 - 1.45: 2856 1.45 - 1.57: 11529 1.57 - 1.69: 0 1.69 - 1.81: 126 Bond restraints: 21024 Sorted by residual: bond pdb=" CA PRO A 108 " pdb=" C PRO A 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 6.09e+00 bond pdb=" CA PRO F 108 " pdb=" C PRO F 108 " ideal model delta sigma weight residual 1.517 1.540 -0.023 9.30e-03 1.16e+04 5.95e+00 bond pdb=" CA PRO D 108 " pdb=" C PRO D 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO C 108 " pdb=" C PRO C 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.79e+00 bond pdb=" CA PRO G 108 " pdb=" C PRO G 108 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.70e+00 ... (remaining 21019 not shown) Histogram of bond angle deviations from ideal: 100.30 - 107.05: 530 107.05 - 113.79: 11654 113.79 - 120.54: 7943 120.54 - 127.28: 8139 127.28 - 134.03: 228 Bond angle restraints: 28494 Sorted by residual: angle pdb=" N ASN G 248 " pdb=" CA ASN G 248 " pdb=" C ASN G 248 " ideal model delta sigma weight residual 111.36 116.08 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ASN C 248 " pdb=" CA ASN C 248 " pdb=" C ASN C 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN B 248 " pdb=" CA ASN B 248 " pdb=" C ASN B 248 " ideal model delta sigma weight residual 111.36 116.07 -4.71 1.09e+00 8.42e-01 1.87e+01 angle pdb=" N ASN E 248 " pdb=" CA ASN E 248 " pdb=" C ASN E 248 " ideal model delta sigma weight residual 111.36 116.04 -4.68 1.09e+00 8.42e-01 1.84e+01 angle pdb=" N ASN I 248 " pdb=" CA ASN I 248 " pdb=" C ASN I 248 " ideal model delta sigma weight residual 111.36 116.01 -4.65 1.09e+00 8.42e-01 1.82e+01 ... (remaining 28489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.50: 11284 15.50 - 30.99: 911 30.99 - 46.49: 180 46.49 - 61.98: 36 61.98 - 77.48: 9 Dihedral angle restraints: 12420 sinusoidal: 4923 harmonic: 7497 Sorted by residual: dihedral pdb=" CA PHE E 70 " pdb=" C PHE E 70 " pdb=" N GLU E 71 " pdb=" CA GLU E 71 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE B 70 " pdb=" C PHE B 70 " pdb=" N GLU B 71 " pdb=" CA GLU B 71 " ideal model delta harmonic sigma weight residual 180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA PHE I 70 " pdb=" C PHE I 70 " pdb=" N GLU I 71 " pdb=" CA GLU I 71 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 12417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1571 0.049 - 0.098: 1044 0.098 - 0.147: 255 0.147 - 0.197: 195 0.197 - 0.246: 103 Chirality restraints: 3168 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE E 127 " pdb=" N ILE E 127 " pdb=" C ILE E 127 " pdb=" CB ILE E 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE I 127 " pdb=" N ILE I 127 " pdb=" C ILE I 127 " pdb=" CB ILE I 127 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 3165 not shown) Planarity restraints: 3600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR F 279 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C THR F 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR F 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN F 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 279 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C THR E 279 " 0.029 2.00e-02 2.50e+03 pdb=" O THR E 279 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN E 280 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 279 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C THR I 279 " -0.029 2.00e-02 2.50e+03 pdb=" O THR I 279 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN I 280 " 0.010 2.00e-02 2.50e+03 ... (remaining 3597 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4989 2.81 - 3.33: 18259 3.33 - 3.86: 36101 3.86 - 4.38: 40324 4.38 - 4.90: 72865 Nonbonded interactions: 172538 Sorted by model distance: nonbonded pdb=" OG SER E 82 " pdb=" OG1 THR F 57 " model vdw 2.289 2.440 nonbonded pdb=" OG SER F 82 " pdb=" OG1 THR G 57 " model vdw 2.289 2.440 nonbonded pdb=" OG SER D 82 " pdb=" OG1 THR E 57 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR A 57 " pdb=" OG SER I 82 " model vdw 2.290 2.440 nonbonded pdb=" OG SER G 82 " pdb=" OG1 THR H 57 " model vdw 2.290 2.440 ... (remaining 172533 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' } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.570 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 46.630 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4972 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 0.044 21024 Z= 0.436 Angle : 1.016 6.166 28494 Z= 0.654 Chirality : 0.081 0.246 3168 Planarity : 0.003 0.028 3600 Dihedral : 11.967 77.477 7650 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.80 % Allowed : 5.84 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -3.69 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.39 (0.12), residues: 1386 loop : -2.35 (0.15), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP C 20 HIS 0.006 0.002 HIS G 103 PHE 0.007 0.002 PHE D 266 TYR 0.016 0.002 TYR F 96 ARG 0.004 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 846 time to evaluate : 2.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7597 (pm20) REVERT: A 44 MET cc_start: 0.5888 (ttm) cc_final: 0.5543 (ttp) REVERT: A 66 THR cc_start: 0.6312 (p) cc_final: 0.6048 (p) REVERT: A 102 GLU cc_start: 0.5810 (mt-10) cc_final: 0.5501 (mt-10) REVERT: A 117 GLN cc_start: 0.5484 (tt0) cc_final: 0.5197 (tt0) REVERT: A 128 GLU cc_start: 0.7959 (pt0) cc_final: 0.7704 (pt0) REVERT: A 152 ARG cc_start: 0.6645 (mmt180) cc_final: 0.6153 (mmt180) REVERT: A 165 LYS cc_start: 0.8397 (tttt) cc_final: 0.7929 (tmtt) REVERT: A 176 LYS cc_start: 0.8041 (mttm) cc_final: 0.7791 (mmtt) REVERT: A 215 ASN cc_start: 0.7870 (m-40) cc_final: 0.7544 (m-40) REVERT: A 217 MET cc_start: 0.8406 (mmt) cc_final: 0.8156 (mpp) REVERT: A 218 TYR cc_start: 0.5527 (m-80) cc_final: 0.5130 (m-10) REVERT: A 285 ASP cc_start: 0.8149 (m-30) cc_final: 0.7809 (m-30) REVERT: A 289 ASP cc_start: 0.5535 (m-30) cc_final: 0.5301 (m-30) REVERT: B 13 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7778 (pm20) REVERT: B 44 MET cc_start: 0.6042 (ttm) cc_final: 0.5803 (tpt) REVERT: B 63 THR cc_start: 0.5293 (p) cc_final: 0.4708 (t) REVERT: B 66 THR cc_start: 0.6471 (p) cc_final: 0.6241 (p) REVERT: B 85 GLU cc_start: 0.5991 (tt0) cc_final: 0.5763 (tm-30) REVERT: B 90 MET cc_start: 0.6274 (ttp) cc_final: 0.5882 (ttp) REVERT: B 94 GLU cc_start: 0.5317 (mt-10) cc_final: 0.4969 (mp0) REVERT: B 130 MET cc_start: 0.4971 (ttp) cc_final: 0.4713 (ttm) REVERT: B 165 LYS cc_start: 0.8160 (tttt) cc_final: 0.7691 (tptt) REVERT: B 167 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7367 (mm-30) REVERT: B 176 LYS cc_start: 0.8293 (mttm) cc_final: 0.8041 (mmtp) REVERT: B 204 GLU cc_start: 0.7897 (tt0) cc_final: 0.7626 (tp30) REVERT: B 215 ASN cc_start: 0.8041 (m-40) cc_final: 0.7738 (m110) REVERT: B 217 MET cc_start: 0.8470 (mmt) cc_final: 0.8183 (mpp) REVERT: B 218 TYR cc_start: 0.6565 (m-80) cc_final: 0.6137 (m-10) REVERT: B 249 LYS cc_start: 0.7976 (tttt) cc_final: 0.7701 (ttpt) REVERT: B 263 ASN cc_start: 0.5734 (t0) cc_final: 0.5491 (t0) REVERT: C 11 GLN cc_start: 0.7054 (pt0) cc_final: 0.6747 (pt0) REVERT: C 13 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8399 (pm20) REVERT: C 36 GLN cc_start: 0.5627 (OUTLIER) cc_final: 0.5412 (tt0) REVERT: C 44 MET cc_start: 0.5681 (ttm) cc_final: 0.5323 (ttp) REVERT: C 45 LYS cc_start: 0.4770 (tttt) cc_final: 0.4542 (tttp) REVERT: C 66 THR cc_start: 0.6345 (p) cc_final: 0.6106 (p) REVERT: C 128 GLU cc_start: 0.7516 (pt0) cc_final: 0.7244 (pt0) REVERT: C 134 ASP cc_start: 0.6710 (m-30) cc_final: 0.6098 (m-30) REVERT: C 165 LYS cc_start: 0.7931 (tttt) cc_final: 0.7485 (tmtt) REVERT: C 175 ARG cc_start: 0.7557 (mmm160) cc_final: 0.7208 (mmm-85) REVERT: C 176 LYS cc_start: 0.8229 (mttm) cc_final: 0.7968 (mmtp) REVERT: C 215 ASN cc_start: 0.7656 (m-40) cc_final: 0.7039 (p0) REVERT: D 13 GLU cc_start: 0.8468 (mt-10) cc_final: 0.7875 (pm20) REVERT: D 44 MET cc_start: 0.5665 (ttm) cc_final: 0.5359 (ttp) REVERT: D 85 GLU cc_start: 0.5947 (tt0) cc_final: 0.5668 (tm-30) REVERT: D 94 GLU cc_start: 0.5781 (mt-10) cc_final: 0.5447 (mt-10) REVERT: D 97 GLU cc_start: 0.6367 (mt-10) cc_final: 0.6034 (mt-10) REVERT: D 130 MET cc_start: 0.5623 (ttp) cc_final: 0.5330 (ttm) REVERT: D 165 LYS cc_start: 0.8343 (tttt) cc_final: 0.7770 (tmmt) REVERT: D 210 ARG cc_start: 0.5599 (mtm180) cc_final: 0.5289 (mtm-85) REVERT: D 215 ASN cc_start: 0.7210 (m-40) cc_final: 0.6743 (p0) REVERT: D 217 MET cc_start: 0.8343 (mmt) cc_final: 0.8142 (mpp) REVERT: D 218 TYR cc_start: 0.5931 (m-80) cc_final: 0.5692 (m-10) REVERT: D 240 ASN cc_start: 0.5734 (t0) cc_final: 0.5447 (t0) REVERT: D 263 ASN cc_start: 0.5975 (t0) cc_final: 0.5669 (t0) REVERT: D 265 TYR cc_start: 0.6834 (t80) cc_final: 0.6575 (t80) REVERT: E 13 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7892 (pm20) REVERT: E 44 MET cc_start: 0.5977 (ttm) cc_final: 0.5751 (tpt) REVERT: E 46 ASN cc_start: 0.5553 (m-40) cc_final: 0.5296 (m110) REVERT: E 85 GLU cc_start: 0.6145 (tt0) cc_final: 0.5906 (tm-30) REVERT: E 90 MET cc_start: 0.6697 (ttp) cc_final: 0.6349 (tmm) REVERT: E 94 GLU cc_start: 0.5164 (mt-10) cc_final: 0.4958 (mt-10) REVERT: E 134 ASP cc_start: 0.6473 (m-30) cc_final: 0.6223 (m-30) REVERT: E 152 ARG cc_start: 0.6504 (mmt180) cc_final: 0.6014 (tpt90) REVERT: E 165 LYS cc_start: 0.8200 (tttt) cc_final: 0.7847 (tmmt) REVERT: E 167 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7488 (mm-30) REVERT: E 204 GLU cc_start: 0.8085 (tt0) cc_final: 0.7873 (pm20) REVERT: E 205 ASP cc_start: 0.7242 (t0) cc_final: 0.6745 (m-30) REVERT: E 214 LEU cc_start: 0.7736 (mt) cc_final: 0.7401 (mt) REVERT: E 215 ASN cc_start: 0.7819 (m-40) cc_final: 0.7361 (m-40) REVERT: E 217 MET cc_start: 0.8449 (mmt) cc_final: 0.7999 (mpp) REVERT: E 218 TYR cc_start: 0.5971 (m-80) cc_final: 0.5654 (m-10) REVERT: E 228 ASP cc_start: 0.9081 (t0) cc_final: 0.8846 (m-30) REVERT: F 11 GLN cc_start: 0.6711 (pt0) cc_final: 0.6478 (pt0) REVERT: F 13 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7583 (pm20) REVERT: F 46 ASN cc_start: 0.5153 (m-40) cc_final: 0.4919 (m110) REVERT: F 63 THR cc_start: 0.5947 (p) cc_final: 0.4919 (t) REVERT: F 85 GLU cc_start: 0.5986 (tt0) cc_final: 0.5735 (tm-30) REVERT: F 102 GLU cc_start: 0.5406 (mt-10) cc_final: 0.5205 (tt0) REVERT: F 165 LYS cc_start: 0.8083 (tttt) cc_final: 0.7575 (tmtt) REVERT: F 176 LYS cc_start: 0.8079 (mttm) cc_final: 0.7848 (mmtp) REVERT: F 215 ASN cc_start: 0.7615 (m-40) cc_final: 0.7390 (m-40) REVERT: F 218 TYR cc_start: 0.4824 (m-80) cc_final: 0.4505 (m-10) REVERT: F 263 ASN cc_start: 0.5721 (t0) cc_final: 0.5219 (t0) REVERT: F 265 TYR cc_start: 0.7020 (t80) cc_final: 0.6807 (t80) REVERT: F 268 ARG cc_start: 0.6927 (mtm-85) cc_final: 0.6648 (mtm-85) REVERT: F 290 LYS cc_start: 0.6379 (mttt) cc_final: 0.6178 (mmtt) REVERT: G 13 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7654 (pm20) REVERT: G 36 GLN cc_start: 0.5845 (OUTLIER) cc_final: 0.5290 (tt0) REVERT: G 42 LYS cc_start: 0.6738 (tttt) cc_final: 0.6270 (mtmm) REVERT: G 46 ASN cc_start: 0.5280 (m-40) cc_final: 0.4989 (m-40) REVERT: G 117 GLN cc_start: 0.5693 (tt0) cc_final: 0.5338 (tt0) REVERT: G 128 GLU cc_start: 0.7320 (pt0) cc_final: 0.7111 (pt0) REVERT: G 165 LYS cc_start: 0.8095 (tttt) cc_final: 0.7761 (tmmt) REVERT: G 176 LYS cc_start: 0.8021 (mttm) cc_final: 0.7804 (mmtt) REVERT: G 194 HIS cc_start: 0.8174 (m90) cc_final: 0.7846 (m90) REVERT: G 205 ASP cc_start: 0.7309 (t0) cc_final: 0.7103 (m-30) REVERT: G 214 LEU cc_start: 0.8011 (mt) cc_final: 0.7705 (mp) REVERT: G 215 ASN cc_start: 0.7742 (m-40) cc_final: 0.7145 (p0) REVERT: G 217 MET cc_start: 0.8705 (mmt) cc_final: 0.8457 (mpp) REVERT: G 218 TYR cc_start: 0.5319 (m-80) cc_final: 0.4944 (m-10) REVERT: H 13 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8167 (pm20) REVERT: H 85 GLU cc_start: 0.6351 (tt0) cc_final: 0.6143 (tm-30) REVERT: H 90 MET cc_start: 0.6389 (ttp) cc_final: 0.6014 (tmm) REVERT: H 92 GLU cc_start: 0.6278 (mt-10) cc_final: 0.5914 (mt-10) REVERT: H 117 GLN cc_start: 0.5846 (tt0) cc_final: 0.5640 (tt0) REVERT: H 130 MET cc_start: 0.5331 (ttp) cc_final: 0.4936 (ttm) REVERT: H 134 ASP cc_start: 0.5997 (m-30) cc_final: 0.5641 (m-30) REVERT: H 165 LYS cc_start: 0.8479 (tttt) cc_final: 0.7972 (tmtt) REVERT: H 174 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8029 (mp0) REVERT: H 176 LYS cc_start: 0.8132 (mttm) cc_final: 0.7919 (mmtp) REVERT: H 205 ASP cc_start: 0.7296 (t0) cc_final: 0.6829 (m-30) REVERT: H 206 TRP cc_start: 0.8687 (p-90) cc_final: 0.8253 (p90) REVERT: H 215 ASN cc_start: 0.7700 (m-40) cc_final: 0.7093 (p0) REVERT: H 217 MET cc_start: 0.8741 (mmt) cc_final: 0.8471 (mpp) REVERT: H 218 TYR cc_start: 0.6189 (m-80) cc_final: 0.5699 (m-10) REVERT: H 263 ASN cc_start: 0.5922 (t0) cc_final: 0.5613 (t0) REVERT: H 266 PHE cc_start: 0.4656 (m-80) cc_final: 0.4421 (m-10) REVERT: H 290 LYS cc_start: 0.6379 (mttt) cc_final: 0.6137 (mttt) REVERT: I 11 GLN cc_start: 0.6335 (pt0) cc_final: 0.6105 (pt0) REVERT: I 13 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7823 (mm-30) REVERT: I 44 MET cc_start: 0.5710 (ttm) cc_final: 0.5137 (tmm) REVERT: I 63 THR cc_start: 0.5651 (p) cc_final: 0.5140 (t) REVERT: I 66 THR cc_start: 0.5868 (p) cc_final: 0.5664 (p) REVERT: I 70 PHE cc_start: 0.4015 (t80) cc_final: 0.3717 (t80) REVERT: I 90 MET cc_start: 0.6686 (ttp) cc_final: 0.6347 (tmm) REVERT: I 97 GLU cc_start: 0.5843 (mt-10) cc_final: 0.5598 (mt-10) REVERT: I 121 ASP cc_start: 0.7415 (t70) cc_final: 0.7137 (m-30) REVERT: I 128 GLU cc_start: 0.7134 (pt0) cc_final: 0.6803 (pt0) REVERT: I 152 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5859 (tpt90) REVERT: I 165 LYS cc_start: 0.8066 (tttt) cc_final: 0.7469 (tmtt) REVERT: I 175 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6800 (mmm-85) REVERT: I 215 ASN cc_start: 0.8019 (m-40) cc_final: 0.7600 (m110) REVERT: I 218 TYR cc_start: 0.5370 (m-80) cc_final: 0.4833 (m-10) REVERT: I 285 ASP cc_start: 0.8373 (m-30) cc_final: 0.8116 (m-30) outliers start: 18 outliers final: 4 residues processed: 855 average time/residue: 0.3780 time to fit residues: 461.9672 Evaluate side-chains 504 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 498 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain G residue 36 GLN Chi-restraints excluded: chain H residue 36 GLN Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 36 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 0.0670 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** C 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN C 243 GLN C 263 ASN D 11 GLN ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 HIS ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 243 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 243 GLN E 263 ASN F 81 HIS F 103 HIS F 117 GLN F 147 GLN F 243 GLN G 11 GLN G 36 GLN ** G 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 117 GLN G 243 GLN G 263 ASN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 HIS H 117 GLN H 243 GLN I 36 GLN ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4962 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 21024 Z= 0.263 Angle : 0.553 7.552 28494 Z= 0.297 Chirality : 0.048 0.189 3168 Planarity : 0.003 0.044 3600 Dihedral : 5.658 88.417 2858 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.32 % Allowed : 13.28 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -3.22 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -2.06 (0.13), residues: 1413 loop : -2.05 (0.15), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 206 HIS 0.008 0.002 HIS C 194 PHE 0.017 0.002 PHE A 209 TYR 0.013 0.001 TYR H 178 ARG 0.006 0.001 ARG I 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 495 time to evaluate : 2.332 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7585 (pm20) REVERT: A 44 MET cc_start: 0.5299 (ttm) cc_final: 0.4967 (ttp) REVERT: A 165 LYS cc_start: 0.8409 (tttt) cc_final: 0.7989 (tmmt) REVERT: A 215 ASN cc_start: 0.7903 (m-40) cc_final: 0.7566 (m-40) REVERT: A 217 MET cc_start: 0.8270 (mmt) cc_final: 0.7967 (mpp) REVERT: A 285 ASP cc_start: 0.8110 (m-30) cc_final: 0.7845 (m-30) REVERT: B 13 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7765 (pm20) REVERT: B 44 MET cc_start: 0.5985 (ttm) cc_final: 0.5759 (ttp) REVERT: B 90 MET cc_start: 0.6169 (ttp) cc_final: 0.5925 (ttp) REVERT: B 94 GLU cc_start: 0.5907 (mt-10) cc_final: 0.5678 (mt-10) REVERT: B 165 LYS cc_start: 0.8492 (tttt) cc_final: 0.8098 (ttpt) REVERT: B 176 LYS cc_start: 0.7857 (mttm) cc_final: 0.7646 (mmtp) REVERT: B 215 ASN cc_start: 0.7518 (m-40) cc_final: 0.7072 (m110) REVERT: B 217 MET cc_start: 0.8245 (mmt) cc_final: 0.7946 (mpp) REVERT: C 97 GLU cc_start: 0.6071 (mt-10) cc_final: 0.5676 (mt-10) REVERT: C 165 LYS cc_start: 0.7922 (tttt) cc_final: 0.7394 (tmtt) REVERT: C 174 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8034 (mp0) REVERT: C 175 ARG cc_start: 0.7229 (mmm160) cc_final: 0.6949 (mtt-85) REVERT: C 176 LYS cc_start: 0.8235 (mttm) cc_final: 0.7939 (mmtp) REVERT: C 215 ASN cc_start: 0.7563 (m-40) cc_final: 0.7210 (m-40) REVERT: C 248 ASN cc_start: 0.7041 (p0) cc_final: 0.6582 (p0) REVERT: C 293 LEU cc_start: 0.5196 (OUTLIER) cc_final: 0.4756 (pp) REVERT: D 13 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7713 (pm20) REVERT: D 44 MET cc_start: 0.5258 (ttm) cc_final: 0.5010 (ttp) REVERT: D 94 GLU cc_start: 0.5806 (mt-10) cc_final: 0.5592 (mt-10) REVERT: D 165 LYS cc_start: 0.8267 (tttt) cc_final: 0.7749 (tmmt) REVERT: D 215 ASN cc_start: 0.7211 (m-40) cc_final: 0.6778 (m110) REVERT: D 217 MET cc_start: 0.8481 (mmt) cc_final: 0.8099 (mpp) REVERT: E 13 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7750 (pm20) REVERT: E 85 GLU cc_start: 0.6294 (tt0) cc_final: 0.6044 (tm-30) REVERT: E 90 MET cc_start: 0.6223 (ttp) cc_final: 0.5873 (tmm) REVERT: E 165 LYS cc_start: 0.8474 (tttt) cc_final: 0.8048 (tmmt) REVERT: E 167 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7393 (mp0) REVERT: E 215 ASN cc_start: 0.7489 (m-40) cc_final: 0.7047 (m110) REVERT: E 217 MET cc_start: 0.8425 (mmt) cc_final: 0.7998 (mpp) REVERT: E 248 ASN cc_start: 0.6652 (p0) cc_final: 0.6187 (p0) REVERT: E 288 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7199 (mt-10) REVERT: F 13 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7695 (pm20) REVERT: F 85 GLU cc_start: 0.6314 (tt0) cc_final: 0.6050 (tm-30) REVERT: F 90 MET cc_start: 0.6347 (ttp) cc_final: 0.6144 (ttp) REVERT: F 165 LYS cc_start: 0.8234 (tttt) cc_final: 0.7753 (tmmt) REVERT: F 215 ASN cc_start: 0.7696 (m-40) cc_final: 0.7392 (m-40) REVERT: F 263 ASN cc_start: 0.5416 (t0) cc_final: 0.5208 (t0) REVERT: G 13 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7980 (pm20) REVERT: G 42 LYS cc_start: 0.7146 (tttt) cc_final: 0.6904 (ttmm) REVERT: G 165 LYS cc_start: 0.8014 (tttt) cc_final: 0.7603 (tmmt) REVERT: G 176 LYS cc_start: 0.7394 (mttm) cc_final: 0.7122 (mmtt) REVERT: G 215 ASN cc_start: 0.7851 (m-40) cc_final: 0.7505 (m110) REVERT: G 217 MET cc_start: 0.8647 (mmt) cc_final: 0.8319 (mpp) REVERT: H 85 GLU cc_start: 0.6174 (tt0) cc_final: 0.5942 (tm-30) REVERT: H 165 LYS cc_start: 0.8427 (tttt) cc_final: 0.7874 (tmtt) REVERT: H 175 ARG cc_start: 0.7260 (mmm160) cc_final: 0.7043 (mmm-85) REVERT: H 215 ASN cc_start: 0.7841 (m-40) cc_final: 0.7292 (m110) REVERT: H 217 MET cc_start: 0.8662 (mmt) cc_final: 0.8245 (mpp) REVERT: I 13 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7855 (pm20) REVERT: I 97 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5695 (mt-10) REVERT: I 159 ARG cc_start: 0.6546 (ttm110) cc_final: 0.6333 (ttp-110) REVERT: I 165 LYS cc_start: 0.8279 (tttt) cc_final: 0.7863 (tmtt) REVERT: I 215 ASN cc_start: 0.8171 (m-40) cc_final: 0.7804 (m-40) REVERT: I 249 LYS cc_start: 0.7788 (ttmt) cc_final: 0.7203 (tttm) REVERT: I 263 ASN cc_start: 0.6144 (t0) cc_final: 0.5916 (t0) REVERT: I 293 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4908 (pp) outliers start: 75 outliers final: 37 residues processed: 557 average time/residue: 0.3054 time to fit residues: 265.3991 Evaluate side-chains 452 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 413 time to evaluate : 2.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 87 GLN Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 150 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 293 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 155 optimal weight: 0.0270 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 103 HIS B 243 GLN B 263 ASN C 36 GLN C 48 ASN C 81 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 GLN C 263 ASN D 11 GLN D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 58 HIS E 81 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN F 46 ASN F 243 GLN G 11 GLN G 48 ASN G 58 HIS G 81 HIS ** G 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN G 147 GLN G 243 GLN G 263 ASN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN ** H 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN I 81 HIS ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 255 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4963 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21024 Z= 0.165 Angle : 0.480 7.276 28494 Z= 0.257 Chirality : 0.047 0.141 3168 Planarity : 0.003 0.036 3600 Dihedral : 4.166 14.725 2844 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.16 % Allowed : 16.91 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.78 (0.14), residues: 2574 helix: None (None), residues: 0 sheet: -1.67 (0.13), residues: 1377 loop : -1.91 (0.14), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 206 HIS 0.006 0.001 HIS E 194 PHE 0.028 0.002 PHE A 209 TYR 0.010 0.001 TYR D 96 ARG 0.005 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 454 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7457 (pm20) REVERT: A 44 MET cc_start: 0.5203 (ttm) cc_final: 0.4987 (tpp) REVERT: A 165 LYS cc_start: 0.8394 (tttt) cc_final: 0.7974 (tmmt) REVERT: A 215 ASN cc_start: 0.7957 (m-40) cc_final: 0.7663 (m-40) REVERT: A 217 MET cc_start: 0.8293 (mmt) cc_final: 0.7986 (mpp) REVERT: A 249 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7986 (ttmm) REVERT: B 13 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7822 (pm20) REVERT: B 90 MET cc_start: 0.6133 (ttp) cc_final: 0.5895 (ttp) REVERT: B 94 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5352 (mt-10) REVERT: B 165 LYS cc_start: 0.8448 (tttt) cc_final: 0.7979 (tmmt) REVERT: B 176 LYS cc_start: 0.8115 (mttm) cc_final: 0.7889 (mmtp) REVERT: B 215 ASN cc_start: 0.7771 (m-40) cc_final: 0.7461 (m110) REVERT: B 217 MET cc_start: 0.8227 (mmt) cc_final: 0.7940 (mpp) REVERT: B 263 ASN cc_start: 0.5525 (t0) cc_final: 0.5271 (t0) REVERT: C 159 ARG cc_start: 0.6344 (ttm110) cc_final: 0.6045 (ttp80) REVERT: C 165 LYS cc_start: 0.8231 (tttt) cc_final: 0.7744 (tmtt) REVERT: C 174 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7863 (mp0) REVERT: C 176 LYS cc_start: 0.8243 (mttm) cc_final: 0.7955 (mmtp) REVERT: C 215 ASN cc_start: 0.7668 (m-40) cc_final: 0.7378 (m-40) REVERT: C 248 ASN cc_start: 0.6900 (p0) cc_final: 0.6391 (p0) REVERT: C 288 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 13 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7814 (pm20) REVERT: D 94 GLU cc_start: 0.5755 (mt-10) cc_final: 0.5512 (mt-10) REVERT: D 165 LYS cc_start: 0.8279 (tttt) cc_final: 0.7798 (tmmt) REVERT: D 215 ASN cc_start: 0.7355 (m-40) cc_final: 0.6992 (m110) REVERT: D 217 MET cc_start: 0.8445 (mmt) cc_final: 0.8099 (mpp) REVERT: D 265 TYR cc_start: 0.6940 (t80) cc_final: 0.6466 (t80) REVERT: E 13 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8060 (pm20) REVERT: E 85 GLU cc_start: 0.6281 (tt0) cc_final: 0.6009 (tm-30) REVERT: E 90 MET cc_start: 0.6061 (ttp) cc_final: 0.5715 (tmm) REVERT: E 165 LYS cc_start: 0.8493 (tttt) cc_final: 0.7990 (tmmt) REVERT: E 167 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7394 (mp0) REVERT: E 215 ASN cc_start: 0.7357 (m-40) cc_final: 0.6933 (m110) REVERT: E 217 MET cc_start: 0.8408 (mmt) cc_final: 0.7985 (mpp) REVERT: E 248 ASN cc_start: 0.6927 (p0) cc_final: 0.6216 (p0) REVERT: E 288 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7122 (mt-10) REVERT: F 90 MET cc_start: 0.6268 (ttp) cc_final: 0.5839 (tmm) REVERT: F 126 ASP cc_start: 0.8049 (t0) cc_final: 0.7500 (m-30) REVERT: F 165 LYS cc_start: 0.8241 (tttt) cc_final: 0.7770 (tmmt) REVERT: F 215 ASN cc_start: 0.7684 (m-40) cc_final: 0.7393 (m-40) REVERT: F 249 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8207 (mtpp) REVERT: G 13 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7971 (pm20) REVERT: G 42 LYS cc_start: 0.7154 (tttt) cc_final: 0.6925 (ttmm) REVERT: G 165 LYS cc_start: 0.7979 (tttt) cc_final: 0.7597 (tmmt) REVERT: G 176 LYS cc_start: 0.7393 (mttm) cc_final: 0.7111 (mmtt) REVERT: G 215 ASN cc_start: 0.7917 (m-40) cc_final: 0.7615 (m110) REVERT: G 217 MET cc_start: 0.8659 (mmt) cc_final: 0.8297 (mpp) REVERT: H 85 GLU cc_start: 0.6210 (tt0) cc_final: 0.5946 (tm-30) REVERT: H 119 ASN cc_start: 0.6755 (t0) cc_final: 0.6458 (t0) REVERT: H 165 LYS cc_start: 0.8420 (tttt) cc_final: 0.7902 (tmtt) REVERT: H 175 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6906 (mmm-85) REVERT: H 215 ASN cc_start: 0.7708 (m-40) cc_final: 0.7320 (m-40) REVERT: H 217 MET cc_start: 0.8648 (mmt) cc_final: 0.8279 (mpp) REVERT: I 13 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8117 (pm20) REVERT: I 159 ARG cc_start: 0.6493 (ttm110) cc_final: 0.6246 (ttm110) REVERT: I 165 LYS cc_start: 0.8310 (tttt) cc_final: 0.7798 (tmmt) REVERT: I 215 ASN cc_start: 0.8390 (m-40) cc_final: 0.8034 (m-40) REVERT: I 263 ASN cc_start: 0.5856 (t0) cc_final: 0.5583 (t0) REVERT: I 275 ASP cc_start: 0.9281 (t0) cc_final: 0.9079 (m-30) REVERT: I 293 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4935 (pp) outliers start: 94 outliers final: 56 residues processed: 523 average time/residue: 0.3227 time to fit residues: 265.2181 Evaluate side-chains 451 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 394 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 155 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 293 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 153 optimal weight: 0.0060 chunk 230 optimal weight: 7.9990 chunk 243 optimal weight: 0.0970 chunk 120 optimal weight: 3.9990 chunk 218 optimal weight: 0.0050 chunk 65 optimal weight: 0.8980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN A 255 HIS B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 117 GLN B 243 GLN B 255 HIS C 48 ASN C 58 HIS C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN E 11 GLN ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN E 58 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN F 243 GLN F 255 HIS G 11 GLN G 58 HIS G 147 GLN G 243 GLN G 263 ASN ** H 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 81 HIS H 243 GLN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 ASN ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 243 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4971 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21024 Z= 0.094 Angle : 0.431 6.972 28494 Z= 0.232 Chirality : 0.046 0.142 3168 Planarity : 0.003 0.037 3600 Dihedral : 3.781 13.653 2844 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.66 % Allowed : 18.33 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.40 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.29 (0.13), residues: 1359 loop : -1.86 (0.14), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 206 HIS 0.004 0.001 HIS E 81 PHE 0.014 0.001 PHE A 209 TYR 0.011 0.001 TYR H 178 ARG 0.004 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 440 time to evaluate : 2.138 Fit side-chains REVERT: A 13 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7447 (pm20) REVERT: A 44 MET cc_start: 0.5158 (ttm) cc_final: 0.4943 (tpp) REVERT: A 165 LYS cc_start: 0.8405 (tttt) cc_final: 0.7948 (tmmt) REVERT: A 215 ASN cc_start: 0.7971 (m-40) cc_final: 0.7718 (m-40) REVERT: B 13 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7806 (pm20) REVERT: B 94 GLU cc_start: 0.5711 (mt-10) cc_final: 0.5322 (mt-10) REVERT: B 165 LYS cc_start: 0.8442 (tttt) cc_final: 0.7957 (tmmt) REVERT: B 176 LYS cc_start: 0.8133 (mttm) cc_final: 0.7915 (mmtp) REVERT: B 206 TRP cc_start: 0.8701 (p90) cc_final: 0.8453 (p-90) REVERT: B 215 ASN cc_start: 0.7761 (m-40) cc_final: 0.7454 (m110) REVERT: B 217 MET cc_start: 0.8296 (mmt) cc_final: 0.7992 (mpp) REVERT: C 159 ARG cc_start: 0.6647 (ttm110) cc_final: 0.6339 (ttp80) REVERT: C 165 LYS cc_start: 0.8264 (tttt) cc_final: 0.7819 (tmtt) REVERT: C 176 LYS cc_start: 0.8257 (mttm) cc_final: 0.7970 (mmtp) REVERT: C 215 ASN cc_start: 0.7591 (m-40) cc_final: 0.7270 (m-40) REVERT: C 248 ASN cc_start: 0.7014 (p0) cc_final: 0.6472 (p0) REVERT: C 288 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 13 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7800 (pm20) REVERT: D 19 VAL cc_start: 0.6459 (t) cc_final: 0.6211 (p) REVERT: D 165 LYS cc_start: 0.8264 (tttt) cc_final: 0.7821 (tmmt) REVERT: D 215 ASN cc_start: 0.7362 (m-40) cc_final: 0.6990 (m110) REVERT: D 217 MET cc_start: 0.8412 (mmt) cc_final: 0.8053 (mpp) REVERT: D 263 ASN cc_start: 0.6085 (t0) cc_final: 0.5503 (t0) REVERT: D 265 TYR cc_start: 0.6907 (t80) cc_final: 0.6580 (t80) REVERT: E 13 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8102 (pm20) REVERT: E 85 GLU cc_start: 0.5928 (tt0) cc_final: 0.5689 (tm-30) REVERT: E 90 MET cc_start: 0.6055 (ttp) cc_final: 0.5721 (tmm) REVERT: E 165 LYS cc_start: 0.8474 (tttt) cc_final: 0.7987 (tmmt) REVERT: E 167 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7326 (mp0) REVERT: E 215 ASN cc_start: 0.7460 (m-40) cc_final: 0.7088 (m110) REVERT: E 217 MET cc_start: 0.8468 (mmt) cc_final: 0.8067 (mpp) REVERT: E 248 ASN cc_start: 0.7304 (p0) cc_final: 0.6942 (p0) REVERT: E 288 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7114 (mt-10) REVERT: F 13 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7568 (pm20) REVERT: F 90 MET cc_start: 0.6288 (ttp) cc_final: 0.5909 (tmm) REVERT: F 126 ASP cc_start: 0.8220 (t0) cc_final: 0.7662 (m-30) REVERT: F 165 LYS cc_start: 0.8289 (tttt) cc_final: 0.7837 (tmmt) REVERT: F 215 ASN cc_start: 0.7588 (m-40) cc_final: 0.7297 (m-40) REVERT: F 257 ASP cc_start: 0.4824 (m-30) cc_final: 0.4476 (m-30) REVERT: G 13 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7974 (pm20) REVERT: G 42 LYS cc_start: 0.7134 (tttt) cc_final: 0.6906 (ttmm) REVERT: G 165 LYS cc_start: 0.7995 (tttt) cc_final: 0.7525 (tmmt) REVERT: G 176 LYS cc_start: 0.7365 (mttm) cc_final: 0.7114 (mmtt) REVERT: G 215 ASN cc_start: 0.7903 (m-40) cc_final: 0.7601 (m110) REVERT: G 217 MET cc_start: 0.8626 (mmt) cc_final: 0.8285 (mpp) REVERT: H 85 GLU cc_start: 0.6300 (tt0) cc_final: 0.6000 (tm-30) REVERT: H 165 LYS cc_start: 0.8389 (tttt) cc_final: 0.7869 (tmtt) REVERT: H 175 ARG cc_start: 0.6913 (mmm160) cc_final: 0.6572 (mmm-85) REVERT: H 215 ASN cc_start: 0.7758 (m-40) cc_final: 0.7408 (m-40) REVERT: H 217 MET cc_start: 0.8650 (mmt) cc_final: 0.8283 (mpp) REVERT: H 249 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7630 (ptmm) REVERT: I 13 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8124 (pm20) REVERT: I 119 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6359 (t0) REVERT: I 159 ARG cc_start: 0.6490 (ttm110) cc_final: 0.6236 (ttm110) REVERT: I 165 LYS cc_start: 0.8444 (tttt) cc_final: 0.8032 (tmmt) REVERT: I 215 ASN cc_start: 0.8437 (m-40) cc_final: 0.8124 (m-40) REVERT: I 263 ASN cc_start: 0.5714 (t0) cc_final: 0.5454 (t0) REVERT: I 288 GLU cc_start: 0.8520 (mt-10) cc_final: 0.7831 (mt-10) outliers start: 60 outliers final: 34 residues processed: 487 average time/residue: 0.3198 time to fit residues: 241.8572 Evaluate side-chains 420 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 385 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 293 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain E residue 293 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 293 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 ASN B 243 GLN B 263 ASN C 46 ASN C 48 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 243 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN E 160 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 263 ASN G 11 GLN G 103 HIS G 263 ASN H 36 GLN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 215 ASN I 243 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4955 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 21024 Z= 0.341 Angle : 0.565 6.476 28494 Z= 0.303 Chirality : 0.049 0.188 3168 Planarity : 0.003 0.056 3600 Dihedral : 4.236 16.038 2844 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.00 % Allowed : 16.38 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.32 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.33 (0.13), residues: 1377 loop : -1.66 (0.15), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP E 206 HIS 0.007 0.002 HIS B 103 PHE 0.020 0.002 PHE C 209 TYR 0.018 0.002 TYR D 96 ARG 0.006 0.001 ARG F 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 385 time to evaluate : 2.284 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7438 (pm20) REVERT: A 44 MET cc_start: 0.5173 (ttm) cc_final: 0.4896 (ptt) REVERT: A 165 LYS cc_start: 0.8407 (tttt) cc_final: 0.8031 (tmmt) REVERT: A 215 ASN cc_start: 0.7383 (m-40) cc_final: 0.7099 (m-40) REVERT: A 288 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 13 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8002 (pm20) REVERT: B 165 LYS cc_start: 0.8445 (tttt) cc_final: 0.8003 (tmmt) REVERT: B 176 LYS cc_start: 0.8114 (mttm) cc_final: 0.7874 (mmtp) REVERT: B 215 ASN cc_start: 0.7215 (m110) cc_final: 0.6792 (m110) REVERT: B 217 MET cc_start: 0.8181 (mmt) cc_final: 0.7873 (mpp) REVERT: C 159 ARG cc_start: 0.6384 (ttm110) cc_final: 0.6048 (ttp80) REVERT: C 165 LYS cc_start: 0.8255 (tttt) cc_final: 0.7808 (tmtt) REVERT: C 176 LYS cc_start: 0.7520 (mttm) cc_final: 0.7275 (mmtp) REVERT: C 198 PHE cc_start: 0.7594 (m-80) cc_final: 0.7325 (m-80) REVERT: C 215 ASN cc_start: 0.7382 (m110) cc_final: 0.7076 (m-40) REVERT: C 248 ASN cc_start: 0.7057 (p0) cc_final: 0.6477 (p0) REVERT: D 13 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7806 (pm20) REVERT: D 165 LYS cc_start: 0.8198 (tttt) cc_final: 0.7668 (tmmt) REVERT: D 215 ASN cc_start: 0.7019 (m-40) cc_final: 0.6713 (m110) REVERT: D 217 MET cc_start: 0.8476 (mmt) cc_final: 0.8169 (mpp) REVERT: D 263 ASN cc_start: 0.5715 (t0) cc_final: 0.5295 (t0) REVERT: D 265 TYR cc_start: 0.6708 (t80) cc_final: 0.6180 (t80) REVERT: E 13 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8194 (pm20) REVERT: E 85 GLU cc_start: 0.5735 (tt0) cc_final: 0.5509 (tm-30) REVERT: E 90 MET cc_start: 0.6327 (ttp) cc_final: 0.6037 (tmm) REVERT: E 165 LYS cc_start: 0.8448 (tttt) cc_final: 0.8029 (tmmt) REVERT: E 167 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7326 (mp0) REVERT: E 215 ASN cc_start: 0.7067 (m-40) cc_final: 0.6667 (m110) REVERT: E 217 MET cc_start: 0.8356 (mmt) cc_final: 0.8043 (mpp) REVERT: E 248 ASN cc_start: 0.7387 (p0) cc_final: 0.6873 (p0) REVERT: E 288 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7003 (mt-10) REVERT: F 90 MET cc_start: 0.6258 (ttp) cc_final: 0.5857 (tmm) REVERT: F 126 ASP cc_start: 0.8046 (t0) cc_final: 0.7615 (m-30) REVERT: F 165 LYS cc_start: 0.8293 (tttt) cc_final: 0.7834 (tmmt) REVERT: F 215 ASN cc_start: 0.7396 (m-40) cc_final: 0.7037 (m-40) REVERT: F 288 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7539 (mt-10) REVERT: G 42 LYS cc_start: 0.7103 (tttt) cc_final: 0.6853 (ttmm) REVERT: G 165 LYS cc_start: 0.8016 (tttt) cc_final: 0.7599 (tmmt) REVERT: G 176 LYS cc_start: 0.7376 (mttm) cc_final: 0.7142 (mmtt) REVERT: G 215 ASN cc_start: 0.7911 (m-40) cc_final: 0.7516 (m110) REVERT: G 217 MET cc_start: 0.8624 (mmt) cc_final: 0.8282 (mpp) REVERT: H 85 GLU cc_start: 0.6360 (tt0) cc_final: 0.6096 (tm-30) REVERT: H 165 LYS cc_start: 0.8402 (tttt) cc_final: 0.7930 (tmtt) REVERT: H 215 ASN cc_start: 0.7423 (m-40) cc_final: 0.6933 (m110) REVERT: H 217 MET cc_start: 0.8428 (mmt) cc_final: 0.8181 (mpp) REVERT: I 13 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8042 (pm20) REVERT: I 159 ARG cc_start: 0.6272 (ttm110) cc_final: 0.6040 (ttm110) REVERT: I 165 LYS cc_start: 0.8279 (tttt) cc_final: 0.7847 (tmtt) REVERT: I 215 ASN cc_start: 0.8108 (m110) cc_final: 0.7793 (m-40) outliers start: 113 outliers final: 73 residues processed: 470 average time/residue: 0.2892 time to fit residues: 213.7027 Evaluate side-chains 450 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 377 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 126 ASP Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 228 ASP Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 3.9990 chunk 219 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN B 263 ASN C 48 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 215 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN F 263 ASN G 11 GLN G 243 GLN G 263 ASN H 48 ASN H 119 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 243 GLN I 263 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4964 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21024 Z= 0.139 Angle : 0.462 7.367 28494 Z= 0.245 Chirality : 0.046 0.222 3168 Planarity : 0.003 0.044 3600 Dihedral : 3.872 15.876 2844 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.63 % Allowed : 18.02 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.17 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.20 (0.13), residues: 1359 loop : -1.61 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 206 HIS 0.007 0.001 HIS A 194 PHE 0.013 0.001 PHE C 209 TYR 0.008 0.001 TYR D 96 ARG 0.006 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 403 time to evaluate : 2.248 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7418 (pm20) REVERT: A 44 MET cc_start: 0.5170 (ttm) cc_final: 0.4896 (ptt) REVERT: A 165 LYS cc_start: 0.8401 (tttt) cc_final: 0.7978 (tmmt) REVERT: A 215 ASN cc_start: 0.7450 (m-40) cc_final: 0.7203 (m-40) REVERT: A 288 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 13 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7990 (pm20) REVERT: B 94 GLU cc_start: 0.5587 (mt-10) cc_final: 0.5194 (mt-10) REVERT: B 165 LYS cc_start: 0.8457 (tttt) cc_final: 0.8090 (ptpt) REVERT: B 176 LYS cc_start: 0.8197 (mttm) cc_final: 0.7982 (mmtp) REVERT: B 215 ASN cc_start: 0.7495 (m-40) cc_final: 0.7153 (m110) REVERT: B 217 MET cc_start: 0.8163 (mmt) cc_final: 0.7853 (mpp) REVERT: C 165 LYS cc_start: 0.8272 (tttt) cc_final: 0.7834 (tmtt) REVERT: C 176 LYS cc_start: 0.8247 (mttm) cc_final: 0.7957 (mmtp) REVERT: C 198 PHE cc_start: 0.7407 (m-80) cc_final: 0.7193 (m-80) REVERT: C 215 ASN cc_start: 0.7440 (m-40) cc_final: 0.7085 (m-40) REVERT: C 248 ASN cc_start: 0.7007 (p0) cc_final: 0.6444 (p0) REVERT: C 257 ASP cc_start: 0.4944 (m-30) cc_final: 0.4693 (m-30) REVERT: D 13 GLU cc_start: 0.8431 (mt-10) cc_final: 0.7806 (pm20) REVERT: D 19 VAL cc_start: 0.6573 (t) cc_final: 0.6369 (p) REVERT: D 165 LYS cc_start: 0.8186 (tttt) cc_final: 0.7681 (tmmt) REVERT: D 215 ASN cc_start: 0.7175 (m110) cc_final: 0.6892 (m110) REVERT: D 217 MET cc_start: 0.8457 (mmt) cc_final: 0.8168 (mpp) REVERT: D 263 ASN cc_start: 0.5675 (t0) cc_final: 0.5235 (t0) REVERT: D 265 TYR cc_start: 0.6869 (t80) cc_final: 0.6318 (t80) REVERT: E 13 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8196 (pm20) REVERT: E 70 PHE cc_start: 0.5031 (OUTLIER) cc_final: 0.4743 (t80) REVERT: E 85 GLU cc_start: 0.5849 (tt0) cc_final: 0.5637 (tm-30) REVERT: E 90 MET cc_start: 0.6084 (ttp) cc_final: 0.5790 (tmm) REVERT: E 94 GLU cc_start: 0.5320 (mt-10) cc_final: 0.4915 (mp0) REVERT: E 165 LYS cc_start: 0.8418 (tttt) cc_final: 0.7944 (tmmt) REVERT: E 167 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7331 (mp0) REVERT: E 215 ASN cc_start: 0.7100 (m-40) cc_final: 0.6696 (m110) REVERT: E 217 MET cc_start: 0.8337 (mmt) cc_final: 0.8036 (mpp) REVERT: E 248 ASN cc_start: 0.7434 (p0) cc_final: 0.6879 (p0) REVERT: E 288 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7143 (mt-10) REVERT: F 90 MET cc_start: 0.6173 (ttp) cc_final: 0.5784 (tmm) REVERT: F 126 ASP cc_start: 0.8227 (t0) cc_final: 0.7728 (m-30) REVERT: F 165 LYS cc_start: 0.8285 (tttt) cc_final: 0.7841 (tmmt) REVERT: F 215 ASN cc_start: 0.7395 (m110) cc_final: 0.7066 (m-40) REVERT: F 263 ASN cc_start: 0.4712 (t0) cc_final: 0.4495 (t0) REVERT: F 265 TYR cc_start: 0.6833 (t80) cc_final: 0.6482 (t80) REVERT: F 288 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7411 (mt-10) REVERT: G 42 LYS cc_start: 0.7091 (tttt) cc_final: 0.6838 (ttmm) REVERT: G 165 LYS cc_start: 0.7955 (tttt) cc_final: 0.7564 (tmmt) REVERT: G 176 LYS cc_start: 0.7351 (mttm) cc_final: 0.7113 (mmtt) REVERT: G 215 ASN cc_start: 0.7838 (m-40) cc_final: 0.7568 (m110) REVERT: G 217 MET cc_start: 0.8618 (mmt) cc_final: 0.8383 (mpp) REVERT: G 228 ASP cc_start: 0.9337 (t0) cc_final: 0.9044 (t0) REVERT: H 85 GLU cc_start: 0.6276 (tt0) cc_final: 0.6015 (tm-30) REVERT: H 119 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6531 (t0) REVERT: H 165 LYS cc_start: 0.8376 (tttt) cc_final: 0.7920 (tmtt) REVERT: H 215 ASN cc_start: 0.7400 (m-40) cc_final: 0.6915 (m110) REVERT: H 217 MET cc_start: 0.8470 (mmt) cc_final: 0.8204 (mpp) REVERT: H 288 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7535 (mt-10) REVERT: I 13 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8045 (pm20) REVERT: I 159 ARG cc_start: 0.6430 (ttm110) cc_final: 0.6181 (ttm110) REVERT: I 165 LYS cc_start: 0.8369 (tttt) cc_final: 0.7962 (tmtt) REVERT: I 215 ASN cc_start: 0.8245 (m110) cc_final: 0.7918 (m-40) REVERT: I 263 ASN cc_start: 0.5665 (t0) cc_final: 0.5381 (t0) outliers start: 82 outliers final: 58 residues processed: 463 average time/residue: 0.2940 time to fit residues: 213.9865 Evaluate side-chains 438 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 378 time to evaluate : 2.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 138 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 205 optimal weight: 0.8980 chunk 136 optimal weight: 0.5980 chunk 242 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 GLN B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN B 263 ASN C 48 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 215 ASN D 243 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN G 263 ASN H 119 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4966 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21024 Z= 0.169 Angle : 0.466 6.420 28494 Z= 0.250 Chirality : 0.046 0.271 3168 Planarity : 0.003 0.040 3600 Dihedral : 3.827 16.089 2844 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.21 % Allowed : 17.57 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -2.04 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.08 (0.14), residues: 1359 loop : -1.56 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 206 HIS 0.004 0.001 HIS D 81 PHE 0.024 0.001 PHE I 209 TYR 0.010 0.001 TYR D 96 ARG 0.009 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 391 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7449 (pm20) REVERT: A 44 MET cc_start: 0.5182 (ttm) cc_final: 0.4905 (ptt) REVERT: A 165 LYS cc_start: 0.8415 (tttt) cc_final: 0.8013 (tmmt) REVERT: A 215 ASN cc_start: 0.7427 (m-40) cc_final: 0.7172 (m-40) REVERT: A 288 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7501 (mt-10) REVERT: B 13 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7993 (pm20) REVERT: B 94 GLU cc_start: 0.5721 (mt-10) cc_final: 0.5331 (mt-10) REVERT: B 165 LYS cc_start: 0.8458 (tttt) cc_final: 0.8100 (ptpt) REVERT: B 176 LYS cc_start: 0.8221 (mttm) cc_final: 0.8006 (mmtp) REVERT: B 215 ASN cc_start: 0.7440 (m110) cc_final: 0.7112 (m110) REVERT: B 217 MET cc_start: 0.8172 (mmt) cc_final: 0.7858 (mpp) REVERT: B 229 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 159 ARG cc_start: 0.6454 (ttm110) cc_final: 0.6154 (ttp80) REVERT: C 165 LYS cc_start: 0.8273 (tttt) cc_final: 0.7838 (tmtt) REVERT: C 176 LYS cc_start: 0.8245 (mttm) cc_final: 0.7955 (mmtp) REVERT: C 198 PHE cc_start: 0.7353 (m-80) cc_final: 0.7111 (m-80) REVERT: C 215 ASN cc_start: 0.7381 (m110) cc_final: 0.7060 (m-40) REVERT: C 248 ASN cc_start: 0.6942 (p0) cc_final: 0.6358 (p0) REVERT: C 257 ASP cc_start: 0.5131 (m-30) cc_final: 0.4843 (m-30) REVERT: D 13 GLU cc_start: 0.8467 (mt-10) cc_final: 0.7812 (pm20) REVERT: D 19 VAL cc_start: 0.6570 (t) cc_final: 0.6365 (p) REVERT: D 165 LYS cc_start: 0.8291 (tttt) cc_final: 0.7826 (tmmt) REVERT: D 215 ASN cc_start: 0.7265 (m-40) cc_final: 0.6926 (m110) REVERT: D 217 MET cc_start: 0.8465 (mmt) cc_final: 0.8173 (mpp) REVERT: D 265 TYR cc_start: 0.6850 (t80) cc_final: 0.6390 (t80) REVERT: E 13 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8191 (pm20) REVERT: E 70 PHE cc_start: 0.5034 (OUTLIER) cc_final: 0.4757 (t80) REVERT: E 90 MET cc_start: 0.6083 (ttp) cc_final: 0.5756 (tmm) REVERT: E 165 LYS cc_start: 0.8417 (tttt) cc_final: 0.7944 (tmmt) REVERT: E 167 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7317 (mp0) REVERT: E 215 ASN cc_start: 0.7054 (m-40) cc_final: 0.6682 (m110) REVERT: E 217 MET cc_start: 0.8353 (mmt) cc_final: 0.8050 (mpp) REVERT: E 248 ASN cc_start: 0.7425 (p0) cc_final: 0.6911 (p0) REVERT: E 288 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7275 (mt-10) REVERT: F 90 MET cc_start: 0.6179 (ttp) cc_final: 0.5796 (tmm) REVERT: F 126 ASP cc_start: 0.8214 (t0) cc_final: 0.7740 (m-30) REVERT: F 165 LYS cc_start: 0.8233 (tttt) cc_final: 0.7789 (tmmt) REVERT: F 215 ASN cc_start: 0.7439 (m-40) cc_final: 0.7095 (m-40) REVERT: F 288 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7447 (mt-10) REVERT: G 42 LYS cc_start: 0.7099 (tttt) cc_final: 0.6853 (ttmm) REVERT: G 165 LYS cc_start: 0.7976 (tttt) cc_final: 0.7478 (tmmt) REVERT: G 176 LYS cc_start: 0.7354 (mttm) cc_final: 0.7113 (mmtt) REVERT: G 215 ASN cc_start: 0.7839 (m-40) cc_final: 0.7538 (m110) REVERT: G 217 MET cc_start: 0.8621 (mmt) cc_final: 0.8387 (mpp) REVERT: G 288 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7587 (mt-10) REVERT: H 85 GLU cc_start: 0.6362 (tt0) cc_final: 0.6101 (tm-30) REVERT: H 165 LYS cc_start: 0.8377 (tttt) cc_final: 0.7913 (tmtt) REVERT: H 215 ASN cc_start: 0.7373 (m-40) cc_final: 0.6878 (m110) REVERT: H 217 MET cc_start: 0.8402 (mmt) cc_final: 0.8035 (mpp) REVERT: H 288 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7725 (mt-10) REVERT: I 13 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8042 (pm20) REVERT: I 159 ARG cc_start: 0.6365 (ttm110) cc_final: 0.6141 (ttm110) REVERT: I 165 LYS cc_start: 0.8375 (tttt) cc_final: 0.7970 (tmtt) REVERT: I 215 ASN cc_start: 0.8256 (m110) cc_final: 0.7920 (m110) outliers start: 95 outliers final: 75 residues processed: 463 average time/residue: 0.2980 time to fit residues: 216.4463 Evaluate side-chains 439 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 363 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 22 optimal weight: 0.3980 chunk 190 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN B 263 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN F 243 GLN F 263 ASN G 263 ASN H 48 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN I 263 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4966 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21024 Z= 0.179 Angle : 0.479 8.480 28494 Z= 0.255 Chirality : 0.047 0.342 3168 Planarity : 0.003 0.047 3600 Dihedral : 3.825 15.520 2844 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.21 % Allowed : 18.19 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -1.00 (0.14), residues: 1341 loop : -1.54 (0.15), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 206 HIS 0.005 0.001 HIS D 81 PHE 0.027 0.001 PHE I 209 TYR 0.012 0.001 TYR I 273 ARG 0.010 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 389 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7446 (pm20) REVERT: A 44 MET cc_start: 0.5240 (ttm) cc_final: 0.4979 (ptt) REVERT: A 165 LYS cc_start: 0.8414 (tttt) cc_final: 0.7960 (tmmt) REVERT: A 215 ASN cc_start: 0.7488 (m-40) cc_final: 0.7233 (m-40) REVERT: A 288 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 13 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7990 (pm20) REVERT: B 94 GLU cc_start: 0.5496 (mt-10) cc_final: 0.5137 (mt-10) REVERT: B 165 LYS cc_start: 0.8482 (tttt) cc_final: 0.8128 (ptpt) REVERT: B 176 LYS cc_start: 0.8234 (mttm) cc_final: 0.7987 (mmtp) REVERT: B 215 ASN cc_start: 0.7497 (m-40) cc_final: 0.7150 (m110) REVERT: B 217 MET cc_start: 0.8164 (mmt) cc_final: 0.7856 (mpp) REVERT: C 159 ARG cc_start: 0.6458 (ttm110) cc_final: 0.6138 (ttp80) REVERT: C 165 LYS cc_start: 0.8274 (tttt) cc_final: 0.7840 (tmtt) REVERT: C 176 LYS cc_start: 0.8231 (mttm) cc_final: 0.7950 (mmtp) REVERT: C 198 PHE cc_start: 0.7344 (m-80) cc_final: 0.7105 (m-80) REVERT: C 215 ASN cc_start: 0.7474 (m-40) cc_final: 0.7109 (m-40) REVERT: C 248 ASN cc_start: 0.7095 (p0) cc_final: 0.6456 (p0) REVERT: C 257 ASP cc_start: 0.5106 (m-30) cc_final: 0.4806 (m-30) REVERT: D 13 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7848 (pm20) REVERT: D 134 ASP cc_start: 0.6607 (m-30) cc_final: 0.6255 (m-30) REVERT: D 147 GLN cc_start: 0.6011 (OUTLIER) cc_final: 0.5763 (tt0) REVERT: D 165 LYS cc_start: 0.8267 (tttt) cc_final: 0.7773 (tmmt) REVERT: D 217 MET cc_start: 0.8473 (mmt) cc_final: 0.8169 (mpp) REVERT: D 265 TYR cc_start: 0.6898 (t80) cc_final: 0.6396 (t80) REVERT: E 13 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8183 (pm20) REVERT: E 70 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.4773 (t80) REVERT: E 90 MET cc_start: 0.5938 (ttp) cc_final: 0.5663 (tmm) REVERT: E 165 LYS cc_start: 0.8412 (tttt) cc_final: 0.7986 (tmmt) REVERT: E 167 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7307 (mp0) REVERT: E 215 ASN cc_start: 0.7022 (m-40) cc_final: 0.6669 (m110) REVERT: E 217 MET cc_start: 0.8352 (mmt) cc_final: 0.8043 (mpp) REVERT: E 248 ASN cc_start: 0.7430 (p0) cc_final: 0.6903 (p0) REVERT: E 288 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7108 (mt-10) REVERT: F 90 MET cc_start: 0.6059 (ttp) cc_final: 0.5674 (tmm) REVERT: F 126 ASP cc_start: 0.8261 (t0) cc_final: 0.7848 (m-30) REVERT: F 165 LYS cc_start: 0.8231 (tttt) cc_final: 0.7796 (tmmt) REVERT: F 215 ASN cc_start: 0.7497 (m110) cc_final: 0.7179 (m-40) REVERT: F 265 TYR cc_start: 0.6816 (t80) cc_final: 0.6505 (t80) REVERT: F 288 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7424 (mt-10) REVERT: G 42 LYS cc_start: 0.7107 (tttt) cc_final: 0.6860 (ttmm) REVERT: G 165 LYS cc_start: 0.7973 (tttt) cc_final: 0.7471 (tmmt) REVERT: G 176 LYS cc_start: 0.7355 (mttm) cc_final: 0.7113 (mmtt) REVERT: G 215 ASN cc_start: 0.7841 (m-40) cc_final: 0.7532 (m110) REVERT: G 217 MET cc_start: 0.8624 (mmt) cc_final: 0.8392 (mpp) REVERT: G 288 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7615 (mt-10) REVERT: H 85 GLU cc_start: 0.6491 (tt0) cc_final: 0.6191 (tm-30) REVERT: H 165 LYS cc_start: 0.8398 (tttt) cc_final: 0.7931 (tmtt) REVERT: H 215 ASN cc_start: 0.7232 (m-40) cc_final: 0.6740 (m110) REVERT: H 217 MET cc_start: 0.8398 (mmt) cc_final: 0.8031 (mpp) REVERT: H 288 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7604 (mt-10) REVERT: I 13 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8045 (pm20) REVERT: I 159 ARG cc_start: 0.6321 (ttm110) cc_final: 0.6098 (ttm110) REVERT: I 165 LYS cc_start: 0.8373 (tttt) cc_final: 0.7970 (tmtt) REVERT: I 215 ASN cc_start: 0.8134 (m110) cc_final: 0.7781 (m110) outliers start: 95 outliers final: 79 residues processed: 461 average time/residue: 0.2965 time to fit residues: 214.4732 Evaluate side-chains 440 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 359 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 204 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN B 263 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 263 ASN G 263 ASN H 215 ASN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4969 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21024 Z= 0.146 Angle : 0.479 9.107 28494 Z= 0.255 Chirality : 0.047 0.331 3168 Planarity : 0.003 0.045 3600 Dihedral : 3.751 15.355 2844 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.85 % Allowed : 19.12 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -1.83 (0.15), residues: 2574 helix: None (None), residues: 0 sheet: -0.92 (0.14), residues: 1359 loop : -1.45 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 206 HIS 0.004 0.001 HIS D 81 PHE 0.026 0.001 PHE I 209 TYR 0.013 0.001 TYR F 218 ARG 0.010 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 378 time to evaluate : 2.537 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7536 (pm20) REVERT: A 44 MET cc_start: 0.5234 (ttm) cc_final: 0.4979 (ptt) REVERT: A 165 LYS cc_start: 0.8412 (tttt) cc_final: 0.7959 (tmmt) REVERT: A 215 ASN cc_start: 0.7522 (m-40) cc_final: 0.7183 (m-40) REVERT: A 288 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 13 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7990 (pm20) REVERT: B 94 GLU cc_start: 0.5504 (mt-10) cc_final: 0.5152 (mt-10) REVERT: B 165 LYS cc_start: 0.8483 (tttt) cc_final: 0.8095 (ptpt) REVERT: B 176 LYS cc_start: 0.8234 (mttm) cc_final: 0.7981 (mmtp) REVERT: B 215 ASN cc_start: 0.7460 (m110) cc_final: 0.7144 (m110) REVERT: B 217 MET cc_start: 0.8163 (mmt) cc_final: 0.7856 (mpp) REVERT: C 159 ARG cc_start: 0.6479 (ttm110) cc_final: 0.6172 (ttp80) REVERT: C 165 LYS cc_start: 0.8276 (tttt) cc_final: 0.7848 (tmtt) REVERT: C 176 LYS cc_start: 0.8291 (mttm) cc_final: 0.7980 (mmtp) REVERT: C 198 PHE cc_start: 0.7337 (m-80) cc_final: 0.7084 (m-80) REVERT: C 215 ASN cc_start: 0.7434 (m110) cc_final: 0.7059 (m-40) REVERT: C 248 ASN cc_start: 0.6947 (p0) cc_final: 0.6262 (p0) REVERT: C 257 ASP cc_start: 0.5117 (m-30) cc_final: 0.4827 (m-30) REVERT: C 288 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7624 (mt-10) REVERT: D 13 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7845 (pm20) REVERT: D 134 ASP cc_start: 0.6220 (m-30) cc_final: 0.5978 (m-30) REVERT: D 147 GLN cc_start: 0.6040 (OUTLIER) cc_final: 0.5781 (tt0) REVERT: D 165 LYS cc_start: 0.8291 (tttt) cc_final: 0.7786 (tmmt) REVERT: D 217 MET cc_start: 0.8478 (mmt) cc_final: 0.8207 (mpp) REVERT: D 265 TYR cc_start: 0.6907 (t80) cc_final: 0.6371 (t80) REVERT: E 13 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8176 (pm20) REVERT: E 70 PHE cc_start: 0.4490 (OUTLIER) cc_final: 0.4093 (t80) REVERT: E 90 MET cc_start: 0.5926 (ttp) cc_final: 0.5670 (tmm) REVERT: E 165 LYS cc_start: 0.8413 (tttt) cc_final: 0.7945 (tmmt) REVERT: E 167 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7293 (mp0) REVERT: E 215 ASN cc_start: 0.7017 (m-40) cc_final: 0.6664 (m110) REVERT: E 217 MET cc_start: 0.8353 (mmt) cc_final: 0.8043 (mpp) REVERT: E 248 ASN cc_start: 0.7450 (p0) cc_final: 0.6976 (p0) REVERT: E 288 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7189 (mt-10) REVERT: F 90 MET cc_start: 0.6058 (ttp) cc_final: 0.5669 (tmm) REVERT: F 126 ASP cc_start: 0.8247 (t0) cc_final: 0.7752 (m-30) REVERT: F 165 LYS cc_start: 0.8207 (tttt) cc_final: 0.7739 (tmmt) REVERT: F 215 ASN cc_start: 0.7508 (m110) cc_final: 0.7219 (m-40) REVERT: F 265 TYR cc_start: 0.6849 (t80) cc_final: 0.6487 (t80) REVERT: F 288 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7448 (mt-10) REVERT: G 42 LYS cc_start: 0.7102 (tttt) cc_final: 0.6855 (ttmm) REVERT: G 165 LYS cc_start: 0.7968 (tttt) cc_final: 0.7487 (tmmt) REVERT: G 176 LYS cc_start: 0.7354 (mttm) cc_final: 0.7117 (mmtt) REVERT: G 215 ASN cc_start: 0.7898 (m-40) cc_final: 0.7642 (m110) REVERT: G 217 MET cc_start: 0.8646 (mmt) cc_final: 0.8385 (mpp) REVERT: G 288 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7507 (mt-10) REVERT: H 85 GLU cc_start: 0.6496 (tt0) cc_final: 0.6197 (tm-30) REVERT: H 165 LYS cc_start: 0.8396 (tttt) cc_final: 0.7936 (tmtt) REVERT: H 198 PHE cc_start: 0.7341 (m-80) cc_final: 0.7074 (m-80) REVERT: H 215 ASN cc_start: 0.7189 (m110) cc_final: 0.6810 (m110) REVERT: H 217 MET cc_start: 0.8391 (mmt) cc_final: 0.8066 (mpp) REVERT: H 288 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7744 (mt-10) REVERT: I 13 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8046 (pm20) REVERT: I 159 ARG cc_start: 0.6339 (ttm110) cc_final: 0.6114 (ttm110) REVERT: I 165 LYS cc_start: 0.8357 (tttt) cc_final: 0.7947 (tmtt) REVERT: I 215 ASN cc_start: 0.8134 (m110) cc_final: 0.7775 (m110) REVERT: I 288 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7834 (mt-10) outliers start: 87 outliers final: 71 residues processed: 443 average time/residue: 0.3014 time to fit residues: 210.6669 Evaluate side-chains 437 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 364 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 186 SER Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.3980 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN B 263 ASN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN F 263 ASN G 263 ASN H 48 ASN H 215 ASN H 243 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4975 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21024 Z= 0.137 Angle : 0.471 8.157 28494 Z= 0.251 Chirality : 0.047 0.307 3168 Planarity : 0.003 0.043 3600 Dihedral : 3.669 15.303 2844 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.63 % Allowed : 19.39 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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 (0.16), residues: 2574 helix: None (None), residues: 0 sheet: -0.79 (0.14), residues: 1377 loop : -1.37 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP F 206 HIS 0.004 0.001 HIS D 81 PHE 0.022 0.001 PHE I 209 TYR 0.012 0.001 TYR F 218 ARG 0.010 0.000 ARG A 159 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 381 time to evaluate : 2.275 Fit side-chains revert: symmetry clash REVERT: A 13 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7529 (pm20) REVERT: A 44 MET cc_start: 0.5236 (ttm) cc_final: 0.4981 (ptt) REVERT: A 165 LYS cc_start: 0.8425 (tttt) cc_final: 0.7970 (tmmt) REVERT: A 215 ASN cc_start: 0.7382 (m-40) cc_final: 0.7105 (m-40) REVERT: A 288 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7534 (mt-10) REVERT: B 13 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7989 (pm20) REVERT: B 92 GLU cc_start: 0.6313 (tt0) cc_final: 0.6108 (tt0) REVERT: B 94 GLU cc_start: 0.5516 (mt-10) cc_final: 0.5035 (mt-10) REVERT: B 165 LYS cc_start: 0.8485 (tttt) cc_final: 0.8106 (ptpt) REVERT: B 175 ARG cc_start: 0.7373 (mmm160) cc_final: 0.7123 (mtp180) REVERT: B 176 LYS cc_start: 0.8191 (mttm) cc_final: 0.7937 (mmtp) REVERT: B 215 ASN cc_start: 0.7520 (m-40) cc_final: 0.7208 (m110) REVERT: B 217 MET cc_start: 0.8287 (mmt) cc_final: 0.8062 (mpp) REVERT: C 159 ARG cc_start: 0.6502 (ttm110) cc_final: 0.6192 (ttp80) REVERT: C 165 LYS cc_start: 0.8586 (tttt) cc_final: 0.8193 (tmtt) REVERT: C 176 LYS cc_start: 0.8293 (mttm) cc_final: 0.7983 (mmtp) REVERT: C 198 PHE cc_start: 0.7405 (m-80) cc_final: 0.7205 (m-80) REVERT: C 215 ASN cc_start: 0.7282 (m-40) cc_final: 0.6937 (m-40) REVERT: C 248 ASN cc_start: 0.6915 (p0) cc_final: 0.6185 (p0) REVERT: C 257 ASP cc_start: 0.5121 (m-30) cc_final: 0.4831 (m-30) REVERT: C 288 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7637 (mt-10) REVERT: D 13 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7843 (pm20) REVERT: D 134 ASP cc_start: 0.6187 (m-30) cc_final: 0.5937 (m-30) REVERT: D 147 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5789 (tt0) REVERT: D 165 LYS cc_start: 0.8270 (tttt) cc_final: 0.7743 (tmmt) REVERT: D 217 MET cc_start: 0.8545 (mmt) cc_final: 0.8272 (mpp) REVERT: D 265 TYR cc_start: 0.6943 (t80) cc_final: 0.6447 (t80) REVERT: E 13 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8140 (pm20) REVERT: E 70 PHE cc_start: 0.4552 (OUTLIER) cc_final: 0.4135 (t80) REVERT: E 90 MET cc_start: 0.5953 (ttp) cc_final: 0.5702 (tmm) REVERT: E 134 ASP cc_start: 0.6403 (m-30) cc_final: 0.6005 (m-30) REVERT: E 165 LYS cc_start: 0.8415 (tttt) cc_final: 0.7950 (tmmt) REVERT: E 167 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7291 (mp0) REVERT: E 215 ASN cc_start: 0.6987 (m-40) cc_final: 0.6609 (m110) REVERT: E 217 MET cc_start: 0.8363 (mmt) cc_final: 0.8053 (mpp) REVERT: E 248 ASN cc_start: 0.7530 (p0) cc_final: 0.7104 (p0) REVERT: E 288 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7194 (mt-10) REVERT: F 90 MET cc_start: 0.6038 (ttp) cc_final: 0.5642 (tmm) REVERT: F 126 ASP cc_start: 0.8245 (t0) cc_final: 0.7753 (m-30) REVERT: F 165 LYS cc_start: 0.8207 (tttt) cc_final: 0.7736 (tmmt) REVERT: F 215 ASN cc_start: 0.7504 (m110) cc_final: 0.7212 (m-40) REVERT: F 265 TYR cc_start: 0.6863 (t80) cc_final: 0.6470 (t80) REVERT: F 288 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7479 (mt-10) REVERT: G 42 LYS cc_start: 0.7094 (tttt) cc_final: 0.6848 (ttmm) REVERT: G 165 LYS cc_start: 0.8297 (tttt) cc_final: 0.7860 (tmmt) REVERT: G 176 LYS cc_start: 0.7781 (mttm) cc_final: 0.7523 (mmtt) REVERT: G 215 ASN cc_start: 0.7848 (m-40) cc_final: 0.7615 (m110) REVERT: G 217 MET cc_start: 0.8616 (mmt) cc_final: 0.8414 (mpp) REVERT: G 288 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7525 (mt-10) REVERT: H 85 GLU cc_start: 0.6498 (tt0) cc_final: 0.6199 (tm-30) REVERT: H 165 LYS cc_start: 0.8385 (tttt) cc_final: 0.7936 (tmtt) REVERT: H 198 PHE cc_start: 0.7364 (m-80) cc_final: 0.7086 (m-80) REVERT: H 215 ASN cc_start: 0.7227 (m-40) cc_final: 0.6829 (m110) REVERT: H 217 MET cc_start: 0.8399 (mmt) cc_final: 0.8073 (mpp) REVERT: H 288 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7694 (mt-10) REVERT: I 13 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8072 (pm20) REVERT: I 159 ARG cc_start: 0.6019 (ttm110) cc_final: 0.5763 (ttm110) REVERT: I 165 LYS cc_start: 0.8488 (tttt) cc_final: 0.8037 (tmtt) REVERT: I 176 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7376 (mmtp) REVERT: I 215 ASN cc_start: 0.8178 (m110) cc_final: 0.7824 (m110) REVERT: I 288 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7845 (mt-10) outliers start: 82 outliers final: 70 residues processed: 446 average time/residue: 0.2977 time to fit residues: 207.1223 Evaluate side-chains 440 residues out of total 2277 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 368 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 87 GLN Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 PHE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 102 GLU Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 46 ASN Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 150 THR Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 260 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain H residue 296 VAL Chi-restraints excluded: chain I residue 11 GLN Chi-restraints excluded: chain I residue 31 SER Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 97 GLU Chi-restraints excluded: chain I residue 121 ASP Chi-restraints excluded: chain I residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 184 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 200 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 205 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 215 ASN B 243 GLN C 58 HIS ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 243 GLN C 263 ASN ** D 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN G 263 ASN H 119 ASN H 243 GLN H 263 ASN I 11 GLN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 243 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098499 restraints weight = 28036.151| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.43 r_work: 0.3250 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 21024 Z= 0.168 Angle : 0.659 59.196 28494 Z= 0.380 Chirality : 0.048 0.589 3168 Planarity : 0.003 0.041 3600 Dihedral : 3.694 26.273 2844 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.45 % Allowed : 19.74 % Favored : 76.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.36 % 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: -1.65 (0.16), residues: 2574 helix: None (None), residues: 0 sheet: -0.77 (0.14), residues: 1377 loop : -1.37 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 206 HIS 0.004 0.001 HIS D 81 PHE 0.019 0.001 PHE I 209 TYR 0.010 0.001 TYR F 218 ARG 0.014 0.001 ARG H 159 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5329.41 seconds wall clock time: 98 minutes 6.39 seconds (5886.39 seconds total)