Starting phenix.real_space_refine on Fri Feb 16 07:43:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zni_11312/02_2024/6zni_11312.pdb" } resolution = 3.6 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= 0.016 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: 3 Type Number sf(0) Gaussians C 9246 2.51 5 N 2438 2.21 5 O 3128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14812 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "C" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "D" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "E" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "G" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "H" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "I" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "J" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "K" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "L" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "M" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "N" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "O" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "Q" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "R" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "S" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "T" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "U" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "V" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "W" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Time building chain proxies: 13.60, per 1000 atoms: 0.92 Number of scatterers: 14812 At special positions: 0 Unit cell: (84.4051, 84.4051, 171.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3128 8.00 N 2438 7.00 C 9246 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: 7.01 Conformation dependent library (CDL) restraints added in 2.8 seconds 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 0 sheets defined 84.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 40 Processing helix chain 'A' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 23 Processing helix chain 'B' and resid 24 through 40 Processing helix chain 'B' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 23 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN C 81 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN E 81 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 23 Processing helix chain 'F' and resid 24 through 40 Processing helix chain 'F' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 24 through 40 Processing helix chain 'G' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 23 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 23 Processing helix chain 'I' and resid 24 through 40 Processing helix chain 'I' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN I 81 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 23 Processing helix chain 'J' and resid 24 through 40 Processing helix chain 'J' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN J 81 " --> pdb=" O ALA J 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 23 Processing helix chain 'K' and resid 24 through 40 Processing helix chain 'K' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN K 81 " --> pdb=" O ALA K 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 23 Processing helix chain 'L' and resid 24 through 40 Processing helix chain 'L' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 23 Processing helix chain 'M' and resid 24 through 40 Processing helix chain 'M' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 23 Processing helix chain 'N' and resid 24 through 40 Processing helix chain 'N' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 23 Processing helix chain 'O' and resid 24 through 40 Processing helix chain 'O' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 23 Processing helix chain 'P' and resid 24 through 40 Processing helix chain 'P' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 23 Processing helix chain 'Q' and resid 24 through 40 Processing helix chain 'Q' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 23 Processing helix chain 'R' and resid 24 through 40 Processing helix chain 'R' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 23 Processing helix chain 'S' and resid 24 through 40 Processing helix chain 'S' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 11 through 23 Processing helix chain 'T' and resid 24 through 40 Processing helix chain 'T' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN T 81 " --> pdb=" O ALA T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 23 Processing helix chain 'U' and resid 24 through 40 Processing helix chain 'U' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 23 Processing helix chain 'V' and resid 24 through 40 Processing helix chain 'V' and resid 43 through 81 removed outlier: 3.622A pdb=" N ASN V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 23 Processing helix chain 'W' and resid 24 through 40 Processing helix chain 'W' and resid 43 through 81 removed outlier: 3.623A pdb=" N ASN W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3864 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2691 1.29 - 1.35: 2277 1.35 - 1.41: 1064 1.41 - 1.48: 2363 1.48 - 1.54: 6624 Bond restraints: 15019 Sorted by residual: bond pdb=" CA THR P 23 " pdb=" CB THR P 23 " ideal model delta sigma weight residual 1.539 1.482 0.058 4.88e-02 4.20e+02 1.39e+00 bond pdb=" CA THR R 23 " pdb=" CB THR R 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.39e+00 bond pdb=" CA THR U 23 " pdb=" CB THR U 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 bond pdb=" CA THR B 23 " pdb=" CB THR B 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 bond pdb=" CA THR S 23 " pdb=" CB THR S 23 " ideal model delta sigma weight residual 1.539 1.482 0.057 4.88e-02 4.20e+02 1.37e+00 ... (remaining 15014 not shown) Histogram of bond angle deviations from ideal: 102.12 - 108.48: 437 108.48 - 114.84: 9246 114.84 - 121.20: 7706 121.20 - 127.56: 3012 127.56 - 133.92: 69 Bond angle restraints: 20470 Sorted by residual: angle pdb=" N ASP D 8 " pdb=" CA ASP D 8 " pdb=" C ASP D 8 " ideal model delta sigma weight residual 111.75 115.40 -3.65 1.28e+00 6.10e-01 8.12e+00 angle pdb=" N ASP M 8 " pdb=" CA ASP M 8 " pdb=" C ASP M 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.06e+00 angle pdb=" N ASP S 8 " pdb=" CA ASP S 8 " pdb=" C ASP S 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.03e+00 angle pdb=" N ASP T 8 " pdb=" CA ASP T 8 " pdb=" C ASP T 8 " ideal model delta sigma weight residual 111.75 115.38 -3.63 1.28e+00 6.10e-01 8.03e+00 angle pdb=" N ASP E 8 " pdb=" CA ASP E 8 " pdb=" C ASP E 8 " ideal model delta sigma weight residual 111.75 115.37 -3.62 1.28e+00 6.10e-01 8.01e+00 ... (remaining 20465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8627 17.14 - 34.27: 412 34.27 - 51.40: 161 51.40 - 68.54: 0 68.54 - 85.67: 23 Dihedral angle restraints: 9223 sinusoidal: 3611 harmonic: 5612 Sorted by residual: dihedral pdb=" CA ASP D 9 " pdb=" C ASP D 9 " pdb=" N TRP D 10 " pdb=" CA TRP D 10 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP B 9 " pdb=" C ASP B 9 " pdb=" N TRP B 10 " pdb=" CA TRP B 10 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA ASP I 9 " pdb=" C ASP I 9 " pdb=" N TRP I 10 " pdb=" CA TRP I 10 " ideal model delta harmonic sigma weight residual 180.00 160.86 19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 9220 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1138 0.025 - 0.049: 1022 0.049 - 0.074: 171 0.074 - 0.099: 38 0.099 - 0.124: 92 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA PRO P 44 " pdb=" N PRO P 44 " pdb=" C PRO P 44 " pdb=" CB PRO P 44 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA PRO S 44 " pdb=" N PRO S 44 " pdb=" C PRO S 44 " pdb=" CB PRO S 44 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO Q 44 " pdb=" N PRO Q 44 " pdb=" C PRO Q 44 " pdb=" CB PRO Q 44 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 2458 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 5 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO H 6 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO H 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 6 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 5 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO E 6 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 6 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 6 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 5 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 6 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 6 " 0.027 5.00e-02 4.00e+02 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 395 2.68 - 3.24: 16130 3.24 - 3.79: 25885 3.79 - 4.35: 28758 4.35 - 4.90: 51677 Nonbonded interactions: 122845 Sorted by model distance: nonbonded pdb=" ND2 ASN G 43 " pdb=" O ASP Q 8 " model vdw 2.130 2.520 nonbonded pdb=" OG SER R 65 " pdb=" ND2 ASN W 81 " model vdw 2.151 2.520 nonbonded pdb=" OG SER C 65 " pdb=" ND2 ASN O 81 " model vdw 2.183 2.520 nonbonded pdb=" OG SER M 65 " pdb=" ND2 ASN R 81 " model vdw 2.190 2.520 nonbonded pdb=" ND2 ASN E 43 " pdb=" O ASP S 8 " model vdw 2.197 2.520 ... (remaining 122840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.930 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 50.070 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15019 Z= 0.467 Angle : 0.612 4.697 20470 Z= 0.368 Chirality : 0.038 0.124 2461 Planarity : 0.006 0.049 2668 Dihedral : 12.209 85.675 5543 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.70 % Allowed : 9.46 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.19), residues: 1840 helix: 1.99 (0.12), residues: 1564 sheet: None (None), residues: 0 loop : -3.28 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP H 10 PHE 0.005 0.001 PHE M 19 TYR 0.010 0.002 TYR M 60 ARG 0.002 0.001 ARG K 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1103 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8226 (t70) REVERT: A 39 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9202 (mmmt) REVERT: A 60 TYR cc_start: 0.8662 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 79 ILE cc_start: 0.9196 (mm) cc_final: 0.8939 (mm) REVERT: B 50 TYR cc_start: 0.8949 (t80) cc_final: 0.8713 (t80) REVERT: C 23 THR cc_start: 0.9317 (m) cc_final: 0.9095 (p) REVERT: C 50 TYR cc_start: 0.9045 (t80) cc_final: 0.8229 (t80) REVERT: C 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8420 (mm-30) REVERT: C 60 TYR cc_start: 0.8918 (OUTLIER) cc_final: 0.7363 (t80) REVERT: D 29 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8226 (mt-10) REVERT: D 49 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8197 (mt-10) REVERT: D 50 TYR cc_start: 0.8988 (t80) cc_final: 0.8235 (t80) REVERT: D 56 GLU cc_start: 0.8948 (tt0) cc_final: 0.8718 (mt-10) REVERT: D 60 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8359 (t80) REVERT: E 25 THR cc_start: 0.8758 (t) cc_final: 0.8554 (t) REVERT: E 30 LEU cc_start: 0.9007 (tp) cc_final: 0.8777 (tp) REVERT: E 45 GLN cc_start: 0.8767 (tp40) cc_final: 0.8479 (tp40) REVERT: E 80 GLN cc_start: 0.8828 (tt0) cc_final: 0.8551 (tp-100) REVERT: F 24 GLN cc_start: 0.9171 (tp-100) cc_final: 0.8716 (tp-100) REVERT: F 45 GLN cc_start: 0.8622 (tp40) cc_final: 0.7672 (tm-30) REVERT: F 49 GLU cc_start: 0.8531 (mt-10) cc_final: 0.7190 (mt-10) REVERT: F 50 TYR cc_start: 0.9082 (t80) cc_final: 0.8854 (t80) REVERT: G 17 GLU cc_start: 0.9121 (mm-30) cc_final: 0.8638 (mm-30) REVERT: G 21 ASP cc_start: 0.8804 (m-30) cc_final: 0.8543 (m-30) REVERT: G 24 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8269 (tp40) REVERT: G 27 GLN cc_start: 0.9088 (mt0) cc_final: 0.8187 (mt0) REVERT: G 45 GLN cc_start: 0.8901 (tp40) cc_final: 0.8436 (tm-30) REVERT: G 49 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7803 (mt-10) REVERT: G 72 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8037 (ttmt) REVERT: H 16 SER cc_start: 0.8726 (m) cc_final: 0.8231 (m) REVERT: H 23 THR cc_start: 0.8850 (m) cc_final: 0.8574 (p) REVERT: H 42 SER cc_start: 0.9014 (p) cc_final: 0.8764 (m) REVERT: H 56 GLU cc_start: 0.9028 (tt0) cc_final: 0.8748 (mm-30) REVERT: H 69 LYS cc_start: 0.8530 (tptp) cc_final: 0.8321 (tptp) REVERT: H 72 LYS cc_start: 0.8662 (ttpt) cc_final: 0.7917 (ttmt) REVERT: I 20 ASP cc_start: 0.8895 (m-30) cc_final: 0.8664 (m-30) REVERT: I 23 THR cc_start: 0.9363 (m) cc_final: 0.9039 (p) REVERT: I 45 GLN cc_start: 0.8974 (tp40) cc_final: 0.8772 (tp40) REVERT: I 56 GLU cc_start: 0.9036 (tt0) cc_final: 0.8611 (mt-10) REVERT: I 60 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8531 (t80) REVERT: I 72 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8081 (ttmt) REVERT: J 50 TYR cc_start: 0.8997 (t80) cc_final: 0.8487 (t80) REVERT: J 56 GLU cc_start: 0.9032 (tt0) cc_final: 0.8692 (mt-10) REVERT: J 72 LYS cc_start: 0.8836 (ttpt) cc_final: 0.8039 (ttmt) REVERT: J 80 GLN cc_start: 0.8842 (tt0) cc_final: 0.8527 (tp-100) REVERT: K 8 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8296 (t70) REVERT: K 21 ASP cc_start: 0.8770 (m-30) cc_final: 0.8350 (m-30) REVERT: K 56 GLU cc_start: 0.9022 (tt0) cc_final: 0.8607 (mt-10) REVERT: K 60 TYR cc_start: 0.8901 (OUTLIER) cc_final: 0.8196 (t80) REVERT: K 72 LYS cc_start: 0.8900 (ttpt) cc_final: 0.7990 (ttmt) REVERT: L 8 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8262 (t70) REVERT: L 24 GLN cc_start: 0.9050 (tp-100) cc_final: 0.8842 (tp40) REVERT: L 45 GLN cc_start: 0.8578 (tp40) cc_final: 0.7943 (tm-30) REVERT: L 56 GLU cc_start: 0.9169 (tt0) cc_final: 0.8662 (mt-10) REVERT: L 60 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8230 (t80) REVERT: L 72 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7866 (ttmt) REVERT: N 8 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8424 (t70) REVERT: N 20 ASP cc_start: 0.9211 (m-30) cc_final: 0.8986 (m-30) REVERT: N 21 ASP cc_start: 0.8810 (m-30) cc_final: 0.8069 (m-30) REVERT: N 27 GLN cc_start: 0.8970 (mt0) cc_final: 0.8444 (mp10) REVERT: N 42 SER cc_start: 0.8789 (p) cc_final: 0.8364 (p) REVERT: N 45 GLN cc_start: 0.8564 (tp40) cc_final: 0.8300 (tp40) REVERT: N 49 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7639 (mt-10) REVERT: O 8 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.8472 (t70) REVERT: O 21 ASP cc_start: 0.8641 (m-30) cc_final: 0.8239 (m-30) REVERT: O 29 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8440 (mt-10) REVERT: O 42 SER cc_start: 0.9049 (p) cc_final: 0.8589 (p) REVERT: O 45 GLN cc_start: 0.8621 (tp40) cc_final: 0.7754 (tm-30) REVERT: O 49 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7413 (mt-10) REVERT: O 80 GLN cc_start: 0.9123 (tt0) cc_final: 0.8816 (tp40) REVERT: Q 45 GLN cc_start: 0.8627 (tp40) cc_final: 0.8222 (tm-30) REVERT: Q 49 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7133 (mt-10) REVERT: R 20 ASP cc_start: 0.9081 (m-30) cc_final: 0.8787 (m-30) REVERT: R 60 TYR cc_start: 0.8999 (OUTLIER) cc_final: 0.8211 (t80) REVERT: R 80 GLN cc_start: 0.8712 (tt0) cc_final: 0.8403 (tp-100) REVERT: S 14 SER cc_start: 0.9129 (t) cc_final: 0.8874 (p) REVERT: S 20 ASP cc_start: 0.9170 (m-30) cc_final: 0.8910 (m-30) REVERT: S 21 ASP cc_start: 0.8632 (m-30) cc_final: 0.8364 (m-30) REVERT: S 46 LEU cc_start: 0.9433 (tp) cc_final: 0.9183 (tt) REVERT: S 56 GLU cc_start: 0.8678 (tt0) cc_final: 0.8392 (mm-30) REVERT: S 60 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8489 (t80) REVERT: S 69 LYS cc_start: 0.8394 (tptp) cc_final: 0.7888 (ttmt) REVERT: S 79 ILE cc_start: 0.9127 (mm) cc_final: 0.8819 (mm) REVERT: S 80 GLN cc_start: 0.8968 (tt0) cc_final: 0.8588 (tp-100) REVERT: T 21 ASP cc_start: 0.8796 (m-30) cc_final: 0.8379 (m-30) REVERT: T 56 GLU cc_start: 0.8852 (tt0) cc_final: 0.8299 (mm-30) REVERT: T 60 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7906 (t80) REVERT: T 69 LYS cc_start: 0.8351 (tptp) cc_final: 0.7880 (tppt) REVERT: U 20 ASP cc_start: 0.9091 (m-30) cc_final: 0.8865 (m-30) REVERT: U 23 THR cc_start: 0.9296 (m) cc_final: 0.8831 (p) REVERT: U 27 GLN cc_start: 0.8758 (mt0) cc_final: 0.8016 (tm-30) REVERT: U 56 GLU cc_start: 0.8886 (tt0) cc_final: 0.8202 (mm-30) REVERT: U 60 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8457 (t80) REVERT: U 69 LYS cc_start: 0.8032 (tptp) cc_final: 0.7676 (tppt) REVERT: V 20 ASP cc_start: 0.9032 (m-30) cc_final: 0.8793 (m-30) REVERT: V 39 LYS cc_start: 0.9403 (mmmt) cc_final: 0.9181 (mmmm) REVERT: V 60 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8281 (t80) REVERT: V 69 LYS cc_start: 0.8217 (tptp) cc_final: 0.7913 (ttmt) REVERT: W 8 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8272 (t70) REVERT: W 16 SER cc_start: 0.8622 (m) cc_final: 0.7831 (m) REVERT: W 17 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8379 (mm-30) REVERT: W 20 ASP cc_start: 0.9191 (m-30) cc_final: 0.8830 (m-30) REVERT: W 21 ASP cc_start: 0.8824 (m-30) cc_final: 0.7585 (m-30) REVERT: W 45 GLN cc_start: 0.8324 (tp40) cc_final: 0.8085 (tm-30) REVERT: W 69 LYS cc_start: 0.8194 (tptp) cc_final: 0.7853 (ttmt) REVERT: W 80 GLN cc_start: 0.8803 (tt0) cc_final: 0.8541 (tp40) outliers start: 46 outliers final: 12 residues processed: 1147 average time/residue: 0.2307 time to fit residues: 400.6763 Evaluate side-chains 986 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 957 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain K residue 8 ASP Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 27 GLN C 27 GLN C 81 ASN D 27 GLN D 81 ASN E 27 GLN E 64 GLN G 27 GLN H 27 GLN I 66 ASN K 27 GLN L 27 GLN M 27 GLN N 27 GLN N 66 ASN N 81 ASN O 27 GLN O 40 ASN P 27 GLN P 80 GLN Q 27 GLN R 27 GLN S 27 GLN S 81 ASN T 27 GLN T 81 ASN U 27 GLN U 81 ASN V 27 GLN W 27 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15019 Z= 0.251 Angle : 0.630 8.433 20470 Z= 0.334 Chirality : 0.039 0.166 2461 Planarity : 0.006 0.049 2668 Dihedral : 6.763 49.371 2059 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.70 % Allowed : 23.91 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.19), residues: 1840 helix: 3.51 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.22 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 10 PHE 0.007 0.001 PHE D 19 TYR 0.015 0.002 TYR W 57 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1001 time to evaluate : 4.413 Fit side-chains revert: symmetry clash REVERT: A 18 THR cc_start: 0.9123 (m) cc_final: 0.8794 (m) REVERT: A 60 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.8191 (t80) REVERT: B 49 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8273 (mt-10) REVERT: C 23 THR cc_start: 0.9277 (m) cc_final: 0.8874 (p) REVERT: C 60 TYR cc_start: 0.8896 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 79 ILE cc_start: 0.9118 (mm) cc_final: 0.8788 (mm) REVERT: D 24 GLN cc_start: 0.8668 (pm20) cc_final: 0.8463 (pm20) REVERT: D 39 LYS cc_start: 0.9479 (mmmt) cc_final: 0.9123 (mmmt) REVERT: D 49 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8262 (mt-10) REVERT: D 50 TYR cc_start: 0.8880 (t80) cc_final: 0.8083 (t80) REVERT: D 80 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8528 (tp-100) REVERT: E 45 GLN cc_start: 0.8683 (tp40) cc_final: 0.8328 (tp40) REVERT: F 45 GLN cc_start: 0.8682 (tp40) cc_final: 0.7879 (tm-30) REVERT: F 49 GLU cc_start: 0.8471 (mt-10) cc_final: 0.7014 (mt-10) REVERT: G 17 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8677 (mm-30) REVERT: G 45 GLN cc_start: 0.8634 (tp40) cc_final: 0.8271 (tm-30) REVERT: G 49 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7850 (mt-10) REVERT: G 72 LYS cc_start: 0.8911 (ttpt) cc_final: 0.7861 (tttt) REVERT: H 20 ASP cc_start: 0.8818 (m-30) cc_final: 0.8520 (m-30) REVERT: H 23 THR cc_start: 0.9285 (m) cc_final: 0.8885 (p) REVERT: H 24 GLN cc_start: 0.7955 (pm20) cc_final: 0.7622 (pm20) REVERT: H 56 GLU cc_start: 0.9009 (tt0) cc_final: 0.8794 (mm-30) REVERT: H 57 TYR cc_start: 0.8707 (t80) cc_final: 0.8434 (t80) REVERT: H 72 LYS cc_start: 0.8723 (ttpt) cc_final: 0.7831 (ttmt) REVERT: I 20 ASP cc_start: 0.8803 (m-30) cc_final: 0.8587 (m-30) REVERT: I 23 THR cc_start: 0.9301 (m) cc_final: 0.8885 (p) REVERT: I 27 GLN cc_start: 0.9077 (mt0) cc_final: 0.8225 (mp10) REVERT: I 42 SER cc_start: 0.8764 (p) cc_final: 0.7949 (p) REVERT: I 60 TYR cc_start: 0.9040 (OUTLIER) cc_final: 0.8370 (t80) REVERT: I 72 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8040 (ttmt) REVERT: J 18 THR cc_start: 0.8990 (m) cc_final: 0.8526 (m) REVERT: J 45 GLN cc_start: 0.8889 (tp40) cc_final: 0.8524 (tm-30) REVERT: J 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8674 (mt-10) REVERT: J 72 LYS cc_start: 0.8957 (ttpt) cc_final: 0.7921 (ttmt) REVERT: K 21 ASP cc_start: 0.8675 (m-30) cc_final: 0.8299 (m-30) REVERT: K 56 GLU cc_start: 0.9015 (tt0) cc_final: 0.8618 (mt-10) REVERT: K 60 TYR cc_start: 0.9014 (OUTLIER) cc_final: 0.7952 (t80) REVERT: K 72 LYS cc_start: 0.8999 (ttpt) cc_final: 0.8061 (ttmt) REVERT: L 8 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8246 (t70) REVERT: L 29 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7876 (mt-10) REVERT: L 45 GLN cc_start: 0.8357 (tp40) cc_final: 0.8133 (tm-30) REVERT: L 49 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7651 (mt-10) REVERT: L 56 GLU cc_start: 0.9134 (tt0) cc_final: 0.8738 (mt-10) REVERT: L 60 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7748 (t80) REVERT: L 72 LYS cc_start: 0.8690 (ttpt) cc_final: 0.7819 (ttmt) REVERT: M 5 VAL cc_start: 0.8449 (t) cc_final: 0.8227 (m) REVERT: M 24 GLN cc_start: 0.8379 (pm20) cc_final: 0.8141 (pm20) REVERT: M 56 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8382 (mm-30) REVERT: N 21 ASP cc_start: 0.8573 (m-30) cc_final: 0.7794 (m-30) REVERT: N 24 GLN cc_start: 0.8415 (pm20) cc_final: 0.8070 (pm20) REVERT: N 27 GLN cc_start: 0.9056 (mt0) cc_final: 0.8375 (mt0) REVERT: N 42 SER cc_start: 0.8935 (p) cc_final: 0.8479 (p) REVERT: N 56 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8012 (mm-30) REVERT: O 21 ASP cc_start: 0.8541 (m-30) cc_final: 0.8043 (m-30) REVERT: O 24 GLN cc_start: 0.8317 (pm20) cc_final: 0.7974 (pm20) REVERT: O 45 GLN cc_start: 0.8505 (tp40) cc_final: 0.7637 (tm-30) REVERT: O 49 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7351 (mt-10) REVERT: O 56 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8577 (mm-30) REVERT: P 56 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8066 (mm-30) REVERT: Q 45 GLN cc_start: 0.8576 (tp40) cc_final: 0.8245 (tm-30) REVERT: Q 49 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7165 (mt-10) REVERT: R 24 GLN cc_start: 0.8580 (pm20) cc_final: 0.8363 (pm20) REVERT: R 45 GLN cc_start: 0.8541 (tp40) cc_final: 0.7896 (tp40) REVERT: R 60 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8287 (t80) REVERT: S 56 GLU cc_start: 0.8772 (tt0) cc_final: 0.8232 (mm-30) REVERT: S 69 LYS cc_start: 0.8831 (tptp) cc_final: 0.7268 (mttm) REVERT: S 72 LYS cc_start: 0.9150 (tmmt) cc_final: 0.8937 (ttpp) REVERT: S 79 ILE cc_start: 0.9078 (mm) cc_final: 0.8819 (mm) REVERT: T 12 LEU cc_start: 0.8547 (mt) cc_final: 0.8211 (mt) REVERT: T 18 THR cc_start: 0.8813 (m) cc_final: 0.8431 (m) REVERT: T 21 ASP cc_start: 0.8750 (m-30) cc_final: 0.8530 (m-30) REVERT: T 60 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7510 (t80) REVERT: T 69 LYS cc_start: 0.8578 (tptp) cc_final: 0.7573 (mttt) REVERT: U 23 THR cc_start: 0.9238 (m) cc_final: 0.8623 (p) REVERT: U 27 GLN cc_start: 0.8902 (mt0) cc_final: 0.8131 (tm-30) REVERT: U 55 SER cc_start: 0.8896 (m) cc_final: 0.8649 (m) REVERT: U 56 GLU cc_start: 0.9014 (tt0) cc_final: 0.8515 (mm-30) REVERT: U 69 LYS cc_start: 0.8466 (tptp) cc_final: 0.7703 (ttmt) REVERT: V 24 GLN cc_start: 0.8427 (pm20) cc_final: 0.8202 (pm20) REVERT: V 39 LYS cc_start: 0.9340 (mmmt) cc_final: 0.9102 (mmmm) REVERT: V 60 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.8319 (t80) REVERT: V 69 LYS cc_start: 0.8494 (tptp) cc_final: 0.7987 (ttmt) REVERT: W 16 SER cc_start: 0.8804 (m) cc_final: 0.8227 (m) REVERT: W 21 ASP cc_start: 0.8645 (m-30) cc_final: 0.8101 (m-30) REVERT: W 23 THR cc_start: 0.9333 (m) cc_final: 0.9020 (p) REVERT: W 24 GLN cc_start: 0.8023 (pm20) cc_final: 0.7580 (pm20) REVERT: W 69 LYS cc_start: 0.8392 (tptp) cc_final: 0.7897 (ttmt) REVERT: W 80 GLN cc_start: 0.8911 (tt0) cc_final: 0.8431 (tp-100) outliers start: 97 outliers final: 62 residues processed: 1042 average time/residue: 0.2278 time to fit residues: 360.5597 Evaluate side-chains 1037 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 966 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 81 ASN Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 64 GLN Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 8 ASP Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 3 VAL Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 67 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 60 TYR Chi-restraints excluded: chain W residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.4980 chunk 51 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 GLN G 40 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN N 81 ASN U 80 GLN U 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15019 Z= 0.212 Angle : 0.644 11.066 20470 Z= 0.326 Chirality : 0.036 0.184 2461 Planarity : 0.006 0.046 2668 Dihedral : 6.456 49.026 2049 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 7.17 % Allowed : 26.32 % Favored : 66.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.64 (0.19), residues: 1840 helix: 3.91 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.44 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 10 PHE 0.005 0.001 PHE D 19 TYR 0.017 0.001 TYR W 57 ARG 0.001 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1109 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 987 time to evaluate : 1.786 Fit side-chains revert: symmetry clash REVERT: A 18 THR cc_start: 0.9005 (m) cc_final: 0.8739 (m) REVERT: A 39 LYS cc_start: 0.9309 (mmmt) cc_final: 0.8977 (mmmm) REVERT: A 54 LEU cc_start: 0.9129 (tp) cc_final: 0.8858 (tt) REVERT: A 56 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8253 (mm-30) REVERT: A 60 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8270 (t80) REVERT: A 79 ILE cc_start: 0.9004 (mm) cc_final: 0.8757 (mm) REVERT: B 50 TYR cc_start: 0.8900 (t80) cc_final: 0.8541 (t80) REVERT: C 21 ASP cc_start: 0.8512 (m-30) cc_final: 0.8070 (m-30) REVERT: C 23 THR cc_start: 0.9219 (m) cc_final: 0.8870 (p) REVERT: C 39 LYS cc_start: 0.9399 (mmmt) cc_final: 0.9192 (mmmt) REVERT: C 40 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8181 (p0) REVERT: C 60 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7726 (t80) REVERT: D 24 GLN cc_start: 0.8771 (pm20) cc_final: 0.8557 (pm20) REVERT: D 32 LEU cc_start: 0.9450 (mm) cc_final: 0.9053 (mm) REVERT: D 50 TYR cc_start: 0.8831 (t80) cc_final: 0.8157 (t80) REVERT: D 80 GLN cc_start: 0.8987 (tp-100) cc_final: 0.8707 (tp-100) REVERT: E 45 GLN cc_start: 0.8546 (tp40) cc_final: 0.8334 (tp40) REVERT: E 56 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8657 (mt-10) REVERT: F 24 GLN cc_start: 0.7727 (pm20) cc_final: 0.7378 (pm20) REVERT: F 45 GLN cc_start: 0.8630 (tp40) cc_final: 0.7813 (tm-30) REVERT: G 21 ASP cc_start: 0.8597 (m-30) cc_final: 0.7673 (m-30) REVERT: G 45 GLN cc_start: 0.8599 (tp40) cc_final: 0.8256 (tm-30) REVERT: G 49 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7906 (mt-10) REVERT: G 56 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8248 (mm-30) REVERT: G 72 LYS cc_start: 0.8875 (ttpt) cc_final: 0.7608 (tttt) REVERT: H 20 ASP cc_start: 0.8837 (m-30) cc_final: 0.8499 (m-30) REVERT: H 23 THR cc_start: 0.9237 (m) cc_final: 0.8809 (p) REVERT: H 24 GLN cc_start: 0.8170 (pm20) cc_final: 0.7947 (pm20) REVERT: H 56 GLU cc_start: 0.8983 (tt0) cc_final: 0.8679 (mm-30) REVERT: H 57 TYR cc_start: 0.8773 (t80) cc_final: 0.8457 (t80) REVERT: H 72 LYS cc_start: 0.8824 (ttpt) cc_final: 0.7930 (ttmt) REVERT: I 23 THR cc_start: 0.9217 (m) cc_final: 0.8996 (p) REVERT: I 27 GLN cc_start: 0.9154 (mt0) cc_final: 0.8922 (mt0) REVERT: I 56 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8462 (mm-30) REVERT: I 60 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8432 (t80) REVERT: I 72 LYS cc_start: 0.8967 (ttpt) cc_final: 0.7957 (ttmt) REVERT: J 18 THR cc_start: 0.8911 (m) cc_final: 0.8449 (m) REVERT: J 56 GLU cc_start: 0.8986 (tt0) cc_final: 0.8638 (mt-10) REVERT: J 72 LYS cc_start: 0.8952 (ttpt) cc_final: 0.7939 (ttmt) REVERT: J 80 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8501 (tp-100) REVERT: K 21 ASP cc_start: 0.8518 (m-30) cc_final: 0.8162 (m-30) REVERT: K 35 ASP cc_start: 0.8896 (m-30) cc_final: 0.8538 (p0) REVERT: K 56 GLU cc_start: 0.8981 (tt0) cc_final: 0.8573 (mt-10) REVERT: K 60 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7650 (t80) REVERT: K 72 LYS cc_start: 0.8994 (ttpt) cc_final: 0.8027 (ttmt) REVERT: L 29 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7987 (mt-10) REVERT: L 40 ASN cc_start: 0.8442 (p0) cc_final: 0.8161 (p0) REVERT: L 49 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7917 (mt-10) REVERT: L 56 GLU cc_start: 0.9159 (tt0) cc_final: 0.8744 (mt-10) REVERT: L 60 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.7761 (t80) REVERT: L 72 LYS cc_start: 0.8661 (ttpt) cc_final: 0.7779 (ttmt) REVERT: M 27 GLN cc_start: 0.9102 (mt0) cc_final: 0.8380 (mp10) REVERT: M 32 LEU cc_start: 0.9396 (mm) cc_final: 0.8934 (mm) REVERT: M 42 SER cc_start: 0.8858 (p) cc_final: 0.8642 (m) REVERT: M 56 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8366 (mm-30) REVERT: M 80 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8825 (tp-100) REVERT: N 21 ASP cc_start: 0.8573 (m-30) cc_final: 0.7912 (m-30) REVERT: N 24 GLN cc_start: 0.8572 (pm20) cc_final: 0.8252 (pm20) REVERT: N 27 GLN cc_start: 0.9074 (mt0) cc_final: 0.8795 (mt0) REVERT: N 42 SER cc_start: 0.8844 (p) cc_final: 0.8189 (m) REVERT: N 56 GLU cc_start: 0.8835 (mt-10) cc_final: 0.7957 (mm-30) REVERT: O 21 ASP cc_start: 0.8467 (m-30) cc_final: 0.7841 (m-30) REVERT: O 24 GLN cc_start: 0.8565 (pm20) cc_final: 0.8164 (pm20) REVERT: O 45 GLN cc_start: 0.8531 (tp40) cc_final: 0.7779 (tm-30) REVERT: O 49 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7322 (mt-10) REVERT: O 56 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8496 (mm-30) REVERT: O 69 LYS cc_start: 0.8387 (tptp) cc_final: 0.7915 (tptp) REVERT: P 35 ASP cc_start: 0.8962 (m-30) cc_final: 0.8695 (p0) REVERT: P 56 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8089 (mm-30) REVERT: Q 35 ASP cc_start: 0.8838 (m-30) cc_final: 0.8536 (p0) REVERT: Q 45 GLN cc_start: 0.8319 (tp40) cc_final: 0.8109 (tm-30) REVERT: Q 49 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7171 (mt-10) REVERT: Q 56 GLU cc_start: 0.8877 (tt0) cc_final: 0.8303 (mm-30) REVERT: R 29 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8052 (mt-10) REVERT: R 45 GLN cc_start: 0.8523 (tp40) cc_final: 0.7898 (tp40) REVERT: R 56 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6201 (mt-10) REVERT: R 60 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8534 (t80) REVERT: S 56 GLU cc_start: 0.8814 (tt0) cc_final: 0.8126 (mm-30) REVERT: S 69 LYS cc_start: 0.8623 (tptp) cc_final: 0.7389 (mttm) REVERT: S 72 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8835 (ttpp) REVERT: S 79 ILE cc_start: 0.9058 (mm) cc_final: 0.8802 (mm) REVERT: T 12 LEU cc_start: 0.8590 (mt) cc_final: 0.8227 (mt) REVERT: T 60 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.7581 (t80) REVERT: T 69 LYS cc_start: 0.8448 (tptp) cc_final: 0.7447 (mttt) REVERT: U 23 THR cc_start: 0.9187 (m) cc_final: 0.8548 (p) REVERT: U 27 GLN cc_start: 0.8894 (mt0) cc_final: 0.8306 (tt0) REVERT: U 55 SER cc_start: 0.8888 (m) cc_final: 0.8660 (m) REVERT: U 56 GLU cc_start: 0.8993 (tt0) cc_final: 0.8426 (mm-30) REVERT: U 69 LYS cc_start: 0.8505 (tptp) cc_final: 0.7759 (ttmt) REVERT: V 39 LYS cc_start: 0.9295 (mmmt) cc_final: 0.9088 (mmmm) REVERT: V 60 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8380 (t80) REVERT: V 69 LYS cc_start: 0.8409 (tptp) cc_final: 0.7324 (mttm) REVERT: V 80 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8728 (tp-100) REVERT: W 21 ASP cc_start: 0.8620 (m-30) cc_final: 0.8104 (m-30) REVERT: W 23 THR cc_start: 0.9389 (m) cc_final: 0.8996 (p) REVERT: W 24 GLN cc_start: 0.8164 (pm20) cc_final: 0.7575 (pm20) REVERT: W 69 LYS cc_start: 0.8339 (tptp) cc_final: 0.7873 (ttmt) REVERT: W 80 GLN cc_start: 0.8853 (tt0) cc_final: 0.8573 (tp-100) outliers start: 122 outliers final: 83 residues processed: 1050 average time/residue: 0.2242 time to fit residues: 357.4586 Evaluate side-chains 1060 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 968 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 55 SER Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN F 40 ASN F 80 GLN G 80 GLN I 27 GLN K 80 GLN P 40 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15019 Z= 0.230 Angle : 0.651 11.400 20470 Z= 0.329 Chirality : 0.037 0.183 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.493 49.188 2047 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 8.52 % Allowed : 26.03 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.69 (0.19), residues: 1840 helix: 3.95 (0.11), residues: 1587 sheet: None (None), residues: 0 loop : -3.51 (0.32), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 10 PHE 0.005 0.001 PHE D 19 TYR 0.019 0.001 TYR W 57 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 973 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8241 (t70) REVERT: A 39 LYS cc_start: 0.9375 (mmmt) cc_final: 0.9093 (mmmm) REVERT: A 56 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8340 (mm-30) REVERT: A 60 TYR cc_start: 0.8816 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 79 ILE cc_start: 0.9078 (mm) cc_final: 0.8793 (mm) REVERT: B 50 TYR cc_start: 0.8930 (t80) cc_final: 0.8631 (t80) REVERT: C 21 ASP cc_start: 0.8524 (m-30) cc_final: 0.8083 (m-30) REVERT: C 23 THR cc_start: 0.9229 (m) cc_final: 0.8857 (p) REVERT: C 40 ASN cc_start: 0.8464 (OUTLIER) cc_final: 0.8110 (p0) REVERT: C 60 TYR cc_start: 0.8868 (OUTLIER) cc_final: 0.7695 (t80) REVERT: D 42 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8117 (m) REVERT: D 50 TYR cc_start: 0.8864 (t80) cc_final: 0.8188 (t80) REVERT: E 45 GLN cc_start: 0.8471 (tp40) cc_final: 0.8234 (tp40) REVERT: E 56 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8460 (mm-30) REVERT: E 80 GLN cc_start: 0.9065 (tp40) cc_final: 0.8733 (tp-100) REVERT: F 24 GLN cc_start: 0.7900 (pm20) cc_final: 0.7485 (pm20) REVERT: F 45 GLN cc_start: 0.8630 (tp40) cc_final: 0.7772 (tm-30) REVERT: G 21 ASP cc_start: 0.8418 (m-30) cc_final: 0.8015 (m-30) REVERT: G 24 GLN cc_start: 0.7635 (pm20) cc_final: 0.7275 (pm20) REVERT: G 45 GLN cc_start: 0.8575 (tp40) cc_final: 0.8252 (tm-30) REVERT: G 49 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7932 (mt-10) REVERT: G 56 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8281 (mm-30) REVERT: G 72 LYS cc_start: 0.8920 (ttpt) cc_final: 0.7973 (ttmt) REVERT: H 20 ASP cc_start: 0.8868 (m-30) cc_final: 0.8569 (m-30) REVERT: H 23 THR cc_start: 0.9229 (m) cc_final: 0.8825 (p) REVERT: H 56 GLU cc_start: 0.8991 (tt0) cc_final: 0.8671 (mm-30) REVERT: H 57 TYR cc_start: 0.8791 (t80) cc_final: 0.8465 (t80) REVERT: H 72 LYS cc_start: 0.8857 (ttpt) cc_final: 0.7925 (ttmt) REVERT: H 80 GLN cc_start: 0.8980 (tp-100) cc_final: 0.8765 (tp-100) REVERT: I 23 THR cc_start: 0.9157 (m) cc_final: 0.8915 (p) REVERT: I 27 GLN cc_start: 0.9147 (mt0) cc_final: 0.8905 (mt0) REVERT: I 56 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8434 (mm-30) REVERT: I 60 TYR cc_start: 0.9120 (OUTLIER) cc_final: 0.8199 (t80) REVERT: I 72 LYS cc_start: 0.8984 (ttpt) cc_final: 0.7944 (ttmt) REVERT: J 56 GLU cc_start: 0.9031 (tt0) cc_final: 0.8689 (mt-10) REVERT: J 72 LYS cc_start: 0.8876 (ttpt) cc_final: 0.7884 (ttmt) REVERT: J 80 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8560 (tp-100) REVERT: K 21 ASP cc_start: 0.8464 (m-30) cc_final: 0.8037 (m-30) REVERT: K 56 GLU cc_start: 0.8976 (tt0) cc_final: 0.8574 (mt-10) REVERT: K 60 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7600 (t80) REVERT: K 72 LYS cc_start: 0.9018 (ttpt) cc_final: 0.7991 (ttmt) REVERT: L 40 ASN cc_start: 0.8397 (p0) cc_final: 0.8098 (p0) REVERT: L 45 GLN cc_start: 0.8407 (tp40) cc_final: 0.7963 (tp40) REVERT: L 56 GLU cc_start: 0.9160 (tt0) cc_final: 0.8753 (mt-10) REVERT: L 60 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7617 (t80) REVERT: L 72 LYS cc_start: 0.8671 (ttpt) cc_final: 0.7767 (ttmt) REVERT: M 56 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8352 (mm-30) REVERT: N 21 ASP cc_start: 0.8544 (m-30) cc_final: 0.7994 (m-30) REVERT: N 24 GLN cc_start: 0.8520 (pm20) cc_final: 0.8288 (pm20) REVERT: N 27 GLN cc_start: 0.8998 (mt0) cc_final: 0.8649 (mt0) REVERT: N 42 SER cc_start: 0.8789 (p) cc_final: 0.8301 (m) REVERT: N 56 GLU cc_start: 0.8761 (mt-10) cc_final: 0.7734 (mm-30) REVERT: O 21 ASP cc_start: 0.8475 (m-30) cc_final: 0.7856 (m-30) REVERT: O 24 GLN cc_start: 0.8536 (pm20) cc_final: 0.8107 (pm20) REVERT: O 45 GLN cc_start: 0.8497 (tp40) cc_final: 0.7789 (tm-30) REVERT: O 49 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7392 (mt-10) REVERT: O 56 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8483 (mm-30) REVERT: O 69 LYS cc_start: 0.8442 (tptp) cc_final: 0.7913 (tptp) REVERT: P 56 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8123 (mm-30) REVERT: Q 24 GLN cc_start: 0.7994 (pm20) cc_final: 0.7715 (pm20) REVERT: Q 35 ASP cc_start: 0.8924 (m-30) cc_final: 0.8694 (m-30) REVERT: Q 49 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7171 (mt-10) REVERT: Q 56 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: R 29 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8039 (mt-10) REVERT: R 45 GLN cc_start: 0.8478 (tp40) cc_final: 0.7744 (tp40) REVERT: R 60 TYR cc_start: 0.9108 (OUTLIER) cc_final: 0.8647 (t80) REVERT: S 56 GLU cc_start: 0.8808 (tt0) cc_final: 0.8070 (mm-30) REVERT: S 69 LYS cc_start: 0.8616 (tptp) cc_final: 0.7435 (mttm) REVERT: S 72 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8828 (ttpp) REVERT: T 12 LEU cc_start: 0.8624 (mt) cc_final: 0.8242 (mt) REVERT: T 60 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.7557 (t80) REVERT: T 69 LYS cc_start: 0.8445 (tptp) cc_final: 0.7436 (mttt) REVERT: U 23 THR cc_start: 0.9282 (m) cc_final: 0.8642 (p) REVERT: U 27 GLN cc_start: 0.8893 (mt0) cc_final: 0.8108 (tm-30) REVERT: U 55 SER cc_start: 0.8888 (m) cc_final: 0.8665 (m) REVERT: U 56 GLU cc_start: 0.8705 (tt0) cc_final: 0.8329 (mm-30) REVERT: U 69 LYS cc_start: 0.8436 (tptp) cc_final: 0.7676 (ttmt) REVERT: V 60 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8296 (t80) REVERT: V 69 LYS cc_start: 0.8422 (tptp) cc_final: 0.7302 (mttm) REVERT: V 80 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8821 (tp-100) REVERT: W 21 ASP cc_start: 0.8602 (m-30) cc_final: 0.8277 (m-30) REVERT: W 23 THR cc_start: 0.9378 (m) cc_final: 0.9011 (p) REVERT: W 24 GLN cc_start: 0.8273 (pm20) cc_final: 0.7973 (pm20) REVERT: W 69 LYS cc_start: 0.8348 (tptp) cc_final: 0.7869 (ttmt) REVERT: W 80 GLN cc_start: 0.8881 (tt0) cc_final: 0.8584 (tp-100) outliers start: 145 outliers final: 111 residues processed: 1048 average time/residue: 0.2355 time to fit residues: 379.0720 Evaluate side-chains 1090 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 967 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 67 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 80 GLN Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 4 THR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Chi-restraints excluded: chain W residue 67 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN F 40 ASN G 80 GLN M 80 GLN N 80 GLN P 40 ASN R 40 ASN S 80 GLN U 80 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15019 Z= 0.195 Angle : 0.674 11.954 20470 Z= 0.333 Chirality : 0.037 0.208 2461 Planarity : 0.006 0.052 2668 Dihedral : 6.454 49.442 2047 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.99 % Allowed : 28.85 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.71 (0.19), residues: 1840 helix: 3.94 (0.11), residues: 1587 sheet: None (None), residues: 0 loop : -3.28 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 10 PHE 0.005 0.001 PHE V 19 TYR 0.020 0.001 TYR W 57 ARG 0.001 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 979 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8121 (t70) REVERT: A 45 GLN cc_start: 0.8496 (tp40) cc_final: 0.8223 (tp40) REVERT: A 54 LEU cc_start: 0.9072 (tp) cc_final: 0.8790 (tt) REVERT: A 56 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8306 (mm-30) REVERT: B 50 TYR cc_start: 0.8893 (t80) cc_final: 0.8668 (t80) REVERT: C 21 ASP cc_start: 0.8643 (m-30) cc_final: 0.8286 (m-30) REVERT: C 23 THR cc_start: 0.9255 (m) cc_final: 0.8892 (p) REVERT: C 60 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7808 (t80) REVERT: D 42 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.7849 (m) REVERT: D 56 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8105 (mm-30) REVERT: E 56 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8333 (mm-30) REVERT: E 80 GLN cc_start: 0.9073 (tp40) cc_final: 0.8740 (tp-100) REVERT: F 24 GLN cc_start: 0.7943 (pm20) cc_final: 0.7484 (pm20) REVERT: F 45 GLN cc_start: 0.8579 (tp40) cc_final: 0.7717 (tm-30) REVERT: G 10 TRP cc_start: 0.8904 (p-90) cc_final: 0.8195 (p-90) REVERT: G 21 ASP cc_start: 0.8424 (m-30) cc_final: 0.7950 (m-30) REVERT: G 24 GLN cc_start: 0.7986 (pm20) cc_final: 0.7578 (pm20) REVERT: G 45 GLN cc_start: 0.8432 (tp40) cc_final: 0.8181 (tm-30) REVERT: G 49 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7833 (mt-10) REVERT: G 56 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8310 (mm-30) REVERT: G 59 LEU cc_start: 0.9352 (mm) cc_final: 0.9105 (mt) REVERT: G 72 LYS cc_start: 0.8888 (ttpt) cc_final: 0.7546 (tttt) REVERT: H 20 ASP cc_start: 0.8869 (m-30) cc_final: 0.8565 (m-30) REVERT: H 23 THR cc_start: 0.9090 (m) cc_final: 0.8700 (p) REVERT: H 39 LYS cc_start: 0.9199 (mmmt) cc_final: 0.8959 (mmmt) REVERT: H 56 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8676 (mm-30) REVERT: H 72 LYS cc_start: 0.8817 (ttpt) cc_final: 0.7863 (ttmt) REVERT: H 80 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8712 (tp-100) REVERT: I 23 THR cc_start: 0.9125 (m) cc_final: 0.8841 (p) REVERT: I 56 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8508 (mm-30) REVERT: I 60 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8478 (t80) REVERT: I 72 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8050 (ttmt) REVERT: J 39 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8971 (mmmt) REVERT: J 56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8641 (mt-10) REVERT: J 72 LYS cc_start: 0.8868 (ttpt) cc_final: 0.7859 (ttmt) REVERT: K 21 ASP cc_start: 0.8436 (m-30) cc_final: 0.7994 (m-30) REVERT: K 56 GLU cc_start: 0.8969 (tt0) cc_final: 0.8591 (mt-10) REVERT: K 60 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7675 (t80) REVERT: K 72 LYS cc_start: 0.9015 (ttpt) cc_final: 0.7949 (ttmt) REVERT: L 40 ASN cc_start: 0.8460 (p0) cc_final: 0.8215 (p0) REVERT: L 45 GLN cc_start: 0.8462 (tp40) cc_final: 0.7754 (tm-30) REVERT: L 49 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8177 (mm-30) REVERT: L 56 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: L 60 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7627 (t80) REVERT: L 72 LYS cc_start: 0.8644 (ttpt) cc_final: 0.7672 (ttmt) REVERT: M 27 GLN cc_start: 0.9139 (mt0) cc_final: 0.8524 (mp10) REVERT: M 56 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8353 (mm-30) REVERT: N 21 ASP cc_start: 0.8514 (m-30) cc_final: 0.8038 (m-30) REVERT: N 24 GLN cc_start: 0.8531 (pm20) cc_final: 0.8303 (pm20) REVERT: N 27 GLN cc_start: 0.8974 (mt0) cc_final: 0.8696 (mt0) REVERT: N 56 GLU cc_start: 0.8843 (mt-10) cc_final: 0.7821 (mm-30) REVERT: O 21 ASP cc_start: 0.8423 (m-30) cc_final: 0.7894 (m-30) REVERT: O 24 GLN cc_start: 0.8589 (pm20) cc_final: 0.8334 (pm20) REVERT: O 45 GLN cc_start: 0.8423 (tp40) cc_final: 0.7698 (tm-30) REVERT: O 49 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7072 (mt-10) REVERT: O 56 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8648 (mt-10) REVERT: O 69 LYS cc_start: 0.8392 (tptp) cc_final: 0.8151 (tptp) REVERT: P 27 GLN cc_start: 0.9014 (mt0) cc_final: 0.8292 (mt0) REVERT: P 35 ASP cc_start: 0.8991 (m-30) cc_final: 0.8667 (p0) REVERT: P 56 GLU cc_start: 0.8751 (mt-10) cc_final: 0.7871 (mm-30) REVERT: P 80 GLN cc_start: 0.9056 (tp40) cc_final: 0.8792 (tp40) REVERT: Q 20 ASP cc_start: 0.9074 (m-30) cc_final: 0.8872 (m-30) REVERT: Q 24 GLN cc_start: 0.8132 (pm20) cc_final: 0.7715 (pm20) REVERT: Q 35 ASP cc_start: 0.8970 (m-30) cc_final: 0.8613 (m-30) REVERT: Q 49 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7806 (mt-10) REVERT: Q 56 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: R 21 ASP cc_start: 0.8252 (m-30) cc_final: 0.7995 (m-30) REVERT: R 29 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7945 (mt-10) REVERT: R 60 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8510 (t80) REVERT: S 56 GLU cc_start: 0.8810 (tt0) cc_final: 0.8032 (mm-30) REVERT: S 69 LYS cc_start: 0.8556 (tptp) cc_final: 0.7438 (mttm) REVERT: S 72 LYS cc_start: 0.9034 (tmmt) cc_final: 0.8809 (ttpp) REVERT: T 12 LEU cc_start: 0.8758 (mt) cc_final: 0.8434 (mt) REVERT: T 45 GLN cc_start: 0.8350 (tp40) cc_final: 0.8015 (tm-30) REVERT: T 60 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7566 (t80) REVERT: T 69 LYS cc_start: 0.8411 (tptp) cc_final: 0.7466 (mttt) REVERT: U 23 THR cc_start: 0.9261 (m) cc_final: 0.8618 (p) REVERT: U 27 GLN cc_start: 0.8866 (mt0) cc_final: 0.8097 (tm-30) REVERT: U 55 SER cc_start: 0.8882 (m) cc_final: 0.8664 (m) REVERT: U 56 GLU cc_start: 0.8676 (tt0) cc_final: 0.8235 (mm-30) REVERT: U 69 LYS cc_start: 0.8422 (tptp) cc_final: 0.7629 (tttt) REVERT: V 60 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8372 (t80) REVERT: V 69 LYS cc_start: 0.8388 (tptp) cc_final: 0.7301 (mttm) REVERT: W 8 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (t0) REVERT: W 21 ASP cc_start: 0.8567 (m-30) cc_final: 0.8206 (m-30) REVERT: W 23 THR cc_start: 0.9326 (m) cc_final: 0.8958 (p) REVERT: W 24 GLN cc_start: 0.8350 (pm20) cc_final: 0.8027 (pm20) REVERT: W 69 LYS cc_start: 0.8305 (tptp) cc_final: 0.7832 (ttmt) outliers start: 119 outliers final: 81 residues processed: 1037 average time/residue: 0.2214 time to fit residues: 350.0158 Evaluate side-chains 1058 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 964 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 80 GLN Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 42 SER Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 8 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.0030 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN I 80 GLN L 80 GLN ** N 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN P 40 ASN Q 40 ASN R 80 GLN S 80 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15019 Z= 0.222 Angle : 0.687 11.969 20470 Z= 0.344 Chirality : 0.039 0.232 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.414 49.412 2045 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 8.11 % Allowed : 28.50 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.66 (0.19), residues: 1840 helix: 3.89 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.15 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 10 PHE 0.004 0.001 PHE O 82 TYR 0.024 0.001 TYR T 50 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 958 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8074 (t70) REVERT: A 45 GLN cc_start: 0.8455 (tp40) cc_final: 0.8252 (tp40) REVERT: A 56 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8379 (mm-30) REVERT: B 50 TYR cc_start: 0.8908 (t80) cc_final: 0.8642 (t80) REVERT: C 21 ASP cc_start: 0.8611 (m-30) cc_final: 0.8244 (m-30) REVERT: C 23 THR cc_start: 0.9222 (m) cc_final: 0.8857 (p) REVERT: C 60 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.7835 (t80) REVERT: D 27 GLN cc_start: 0.9052 (mt0) cc_final: 0.8631 (mt0) REVERT: D 42 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.7921 (m) REVERT: D 56 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8114 (mm-30) REVERT: E 27 GLN cc_start: 0.9041 (mt0) cc_final: 0.8587 (mt0) REVERT: E 42 SER cc_start: 0.9414 (m) cc_final: 0.8519 (m) REVERT: E 56 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8480 (mm-30) REVERT: E 80 GLN cc_start: 0.9030 (tp40) cc_final: 0.8717 (tp-100) REVERT: F 24 GLN cc_start: 0.7999 (pm20) cc_final: 0.7498 (pm20) REVERT: F 45 GLN cc_start: 0.8590 (tp40) cc_final: 0.7731 (tm-30) REVERT: G 21 ASP cc_start: 0.8394 (m-30) cc_final: 0.7885 (m-30) REVERT: G 24 GLN cc_start: 0.8153 (pm20) cc_final: 0.7641 (pm20) REVERT: G 45 GLN cc_start: 0.8452 (tp40) cc_final: 0.8197 (tm-30) REVERT: G 49 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7877 (mt-10) REVERT: G 56 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8303 (mm-30) REVERT: G 59 LEU cc_start: 0.9350 (mm) cc_final: 0.9116 (mt) REVERT: G 72 LYS cc_start: 0.8962 (ttpt) cc_final: 0.7927 (ttmt) REVERT: H 20 ASP cc_start: 0.8907 (m-30) cc_final: 0.8585 (m-30) REVERT: H 23 THR cc_start: 0.9080 (m) cc_final: 0.8693 (p) REVERT: H 39 LYS cc_start: 0.9245 (mmmt) cc_final: 0.9040 (mmmt) REVERT: H 56 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8668 (mm-30) REVERT: H 72 LYS cc_start: 0.8831 (ttpt) cc_final: 0.7854 (ttmt) REVERT: H 80 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8753 (tp-100) REVERT: I 8 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.8525 (t0) REVERT: I 23 THR cc_start: 0.9144 (m) cc_final: 0.8808 (p) REVERT: I 56 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8422 (mm-30) REVERT: I 60 TYR cc_start: 0.9138 (OUTLIER) cc_final: 0.8126 (t80) REVERT: I 72 LYS cc_start: 0.8991 (ttpt) cc_final: 0.8052 (ttmt) REVERT: J 27 GLN cc_start: 0.8998 (mt0) cc_final: 0.8427 (mp10) REVERT: J 39 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8952 (mmmt) REVERT: J 56 GLU cc_start: 0.9020 (tt0) cc_final: 0.8675 (mt-10) REVERT: J 72 LYS cc_start: 0.8886 (ttpt) cc_final: 0.7848 (ttmt) REVERT: J 80 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8753 (tp40) REVERT: K 21 ASP cc_start: 0.8371 (m-30) cc_final: 0.8130 (m-30) REVERT: K 35 ASP cc_start: 0.8996 (m-30) cc_final: 0.8742 (m-30) REVERT: K 56 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8602 (mt-10) REVERT: K 60 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7600 (t80) REVERT: K 72 LYS cc_start: 0.9023 (ttpt) cc_final: 0.7984 (ttmt) REVERT: L 40 ASN cc_start: 0.8505 (p0) cc_final: 0.8273 (p0) REVERT: L 49 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8354 (mm-30) REVERT: L 56 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8753 (mt-10) REVERT: L 60 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.7658 (t80) REVERT: L 72 LYS cc_start: 0.8662 (ttpt) cc_final: 0.7680 (ttmt) REVERT: M 56 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8358 (mm-30) REVERT: N 21 ASP cc_start: 0.8507 (m-30) cc_final: 0.8064 (m-30) REVERT: N 27 GLN cc_start: 0.8974 (mt0) cc_final: 0.8682 (mt0) REVERT: N 56 GLU cc_start: 0.8850 (mt-10) cc_final: 0.7985 (mm-30) REVERT: O 21 ASP cc_start: 0.8437 (m-30) cc_final: 0.7896 (m-30) REVERT: O 24 GLN cc_start: 0.8699 (pm20) cc_final: 0.8445 (pm20) REVERT: O 45 GLN cc_start: 0.8448 (tp40) cc_final: 0.7730 (tm-30) REVERT: O 49 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7166 (mt-10) REVERT: O 56 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8650 (mt-10) REVERT: O 69 LYS cc_start: 0.8364 (tptp) cc_final: 0.8131 (tptp) REVERT: P 27 GLN cc_start: 0.9015 (mt0) cc_final: 0.8343 (mt0) REVERT: P 35 ASP cc_start: 0.8987 (m-30) cc_final: 0.8764 (p0) REVERT: P 80 GLN cc_start: 0.9061 (tp40) cc_final: 0.8790 (tp-100) REVERT: Q 24 GLN cc_start: 0.8243 (pm20) cc_final: 0.8018 (pm20) REVERT: Q 35 ASP cc_start: 0.8946 (m-30) cc_final: 0.8529 (m-30) REVERT: Q 56 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: R 21 ASP cc_start: 0.8324 (m-30) cc_final: 0.8055 (m-30) REVERT: R 29 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7852 (mt-10) REVERT: R 60 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8502 (t80) REVERT: S 56 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: S 69 LYS cc_start: 0.8574 (tptp) cc_final: 0.7432 (mttm) REVERT: S 72 LYS cc_start: 0.9062 (tmmt) cc_final: 0.8821 (ttpp) REVERT: T 45 GLN cc_start: 0.8326 (tp40) cc_final: 0.7976 (tm-30) REVERT: T 56 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8088 (mm-30) REVERT: T 60 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.7680 (t80) REVERT: T 69 LYS cc_start: 0.8417 (tptp) cc_final: 0.7470 (mttt) REVERT: U 23 THR cc_start: 0.9340 (m) cc_final: 0.8671 (p) REVERT: U 27 GLN cc_start: 0.8853 (mt0) cc_final: 0.8107 (tm-30) REVERT: U 54 LEU cc_start: 0.9020 (tp) cc_final: 0.8793 (tt) REVERT: U 56 GLU cc_start: 0.8703 (tt0) cc_final: 0.8031 (mm-30) REVERT: U 69 LYS cc_start: 0.8444 (tptp) cc_final: 0.7374 (mttt) REVERT: V 14 SER cc_start: 0.8986 (t) cc_final: 0.8523 (p) REVERT: V 60 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8276 (t80) REVERT: V 69 LYS cc_start: 0.8371 (tptp) cc_final: 0.7245 (mttm) REVERT: V 79 ILE cc_start: 0.8968 (mm) cc_final: 0.8698 (mm) REVERT: W 21 ASP cc_start: 0.8566 (m-30) cc_final: 0.8199 (m-30) REVERT: W 23 THR cc_start: 0.9336 (m) cc_final: 0.8972 (p) REVERT: W 24 GLN cc_start: 0.8434 (pm20) cc_final: 0.8090 (pm20) REVERT: W 69 LYS cc_start: 0.8316 (tptp) cc_final: 0.7830 (ttmt) outliers start: 138 outliers final: 96 residues processed: 1033 average time/residue: 0.2156 time to fit residues: 340.3652 Evaluate side-chains 1061 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 949 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 8 ASP Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 11 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 8 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN D 40 ASN E 40 ASN F 40 ASN J 51 GLN N 80 GLN N 81 ASN P 40 ASN Q 40 ASN R 40 ASN S 80 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15019 Z= 0.259 Angle : 0.714 12.091 20470 Z= 0.361 Chirality : 0.040 0.232 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.491 49.439 2045 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 8.70 % Allowed : 29.44 % Favored : 61.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.53 (0.19), residues: 1840 helix: 3.78 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -3.04 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 10 PHE 0.004 0.001 PHE N 82 TYR 0.025 0.002 TYR T 50 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 963 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8206 (t70) REVERT: A 45 GLN cc_start: 0.8628 (tp40) cc_final: 0.8420 (tp40) REVERT: A 56 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8373 (mm-30) REVERT: B 50 TYR cc_start: 0.8911 (t80) cc_final: 0.8706 (t80) REVERT: C 21 ASP cc_start: 0.8624 (m-30) cc_final: 0.8245 (m-30) REVERT: C 23 THR cc_start: 0.9214 (m) cc_final: 0.8853 (p) REVERT: C 60 TYR cc_start: 0.8845 (OUTLIER) cc_final: 0.7769 (t80) REVERT: D 27 GLN cc_start: 0.8985 (mt0) cc_final: 0.8528 (mt0) REVERT: D 42 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.7975 (m) REVERT: D 50 TYR cc_start: 0.8869 (t80) cc_final: 0.8133 (t80) REVERT: E 27 GLN cc_start: 0.9078 (mt0) cc_final: 0.8690 (mt0) REVERT: E 42 SER cc_start: 0.9365 (m) cc_final: 0.8496 (m) REVERT: E 80 GLN cc_start: 0.9027 (tp40) cc_final: 0.8712 (tp-100) REVERT: F 45 GLN cc_start: 0.8644 (tp40) cc_final: 0.7755 (tm-30) REVERT: G 24 GLN cc_start: 0.8348 (pm20) cc_final: 0.8131 (pm20) REVERT: G 45 GLN cc_start: 0.8582 (tp40) cc_final: 0.8228 (tm-30) REVERT: G 49 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7844 (mt-10) REVERT: G 56 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8270 (mm-30) REVERT: G 59 LEU cc_start: 0.9374 (mm) cc_final: 0.9153 (mt) REVERT: G 72 LYS cc_start: 0.8962 (ttpt) cc_final: 0.7877 (ttmt) REVERT: H 20 ASP cc_start: 0.8901 (m-30) cc_final: 0.8562 (m-30) REVERT: H 23 THR cc_start: 0.9069 (m) cc_final: 0.8681 (p) REVERT: H 56 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8665 (mm-30) REVERT: H 72 LYS cc_start: 0.8843 (ttpt) cc_final: 0.7850 (ttmt) REVERT: H 80 GLN cc_start: 0.9004 (tp-100) cc_final: 0.8792 (tp-100) REVERT: I 8 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8509 (t0) REVERT: I 23 THR cc_start: 0.9125 (m) cc_final: 0.8792 (p) REVERT: I 56 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8440 (mm-30) REVERT: I 60 TYR cc_start: 0.9151 (OUTLIER) cc_final: 0.8434 (t80) REVERT: I 72 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8054 (ttmt) REVERT: J 18 THR cc_start: 0.8953 (m) cc_final: 0.8524 (m) REVERT: J 39 LYS cc_start: 0.9327 (mmtt) cc_final: 0.8958 (mmmt) REVERT: J 56 GLU cc_start: 0.9034 (tt0) cc_final: 0.8668 (mt-10) REVERT: J 72 LYS cc_start: 0.8908 (ttpt) cc_final: 0.7854 (ttmt) REVERT: K 21 ASP cc_start: 0.8477 (m-30) cc_final: 0.8159 (m-30) REVERT: K 35 ASP cc_start: 0.9013 (m-30) cc_final: 0.8748 (m-30) REVERT: K 56 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: K 60 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7598 (t80) REVERT: K 72 LYS cc_start: 0.9043 (ttpt) cc_final: 0.7991 (ttmt) REVERT: L 40 ASN cc_start: 0.8482 (p0) cc_final: 0.8264 (p0) REVERT: L 56 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8746 (mt-10) REVERT: L 60 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7662 (t80) REVERT: L 72 LYS cc_start: 0.8675 (ttpt) cc_final: 0.7756 (ttmt) REVERT: M 56 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8355 (mm-30) REVERT: N 27 GLN cc_start: 0.8978 (mt0) cc_final: 0.8691 (mt0) REVERT: N 56 GLU cc_start: 0.8836 (mt-10) cc_final: 0.7921 (mm-30) REVERT: O 21 ASP cc_start: 0.8450 (m-30) cc_final: 0.7909 (m-30) REVERT: O 24 GLN cc_start: 0.8805 (pm20) cc_final: 0.8539 (pm20) REVERT: O 45 GLN cc_start: 0.8396 (tp40) cc_final: 0.7746 (tm-30) REVERT: O 49 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7247 (mt-10) REVERT: O 56 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8806 (mt-10) REVERT: O 69 LYS cc_start: 0.8373 (tptp) cc_final: 0.8134 (tptp) REVERT: P 27 GLN cc_start: 0.9027 (mt0) cc_final: 0.8306 (mt0) REVERT: P 56 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8124 (mm-30) REVERT: P 80 GLN cc_start: 0.9079 (tp40) cc_final: 0.8607 (tp-100) REVERT: Q 24 GLN cc_start: 0.8258 (pm20) cc_final: 0.8030 (pm20) REVERT: Q 35 ASP cc_start: 0.8943 (m-30) cc_final: 0.8501 (m-30) REVERT: Q 56 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8619 (mt-10) REVERT: R 29 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7948 (mt-10) REVERT: R 60 TYR cc_start: 0.9080 (OUTLIER) cc_final: 0.8482 (t80) REVERT: S 56 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: S 69 LYS cc_start: 0.8584 (tptp) cc_final: 0.7433 (mttm) REVERT: S 72 LYS cc_start: 0.9066 (tmmt) cc_final: 0.8840 (ttpp) REVERT: T 45 GLN cc_start: 0.8401 (tp40) cc_final: 0.8034 (tm-30) REVERT: T 60 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.7693 (t80) REVERT: T 69 LYS cc_start: 0.8429 (tptp) cc_final: 0.7466 (mttt) REVERT: U 23 THR cc_start: 0.9327 (m) cc_final: 0.8675 (p) REVERT: U 27 GLN cc_start: 0.8861 (mt0) cc_final: 0.8306 (tt0) REVERT: U 54 LEU cc_start: 0.9054 (tp) cc_final: 0.8810 (tt) REVERT: U 69 LYS cc_start: 0.8421 (tptp) cc_final: 0.7276 (mttt) REVERT: V 60 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8334 (t80) REVERT: V 69 LYS cc_start: 0.8380 (tptp) cc_final: 0.7757 (ttmt) REVERT: V 79 ILE cc_start: 0.8993 (mm) cc_final: 0.8731 (mm) REVERT: W 21 ASP cc_start: 0.8573 (m-30) cc_final: 0.8171 (m-30) REVERT: W 23 THR cc_start: 0.9296 (m) cc_final: 0.8915 (p) REVERT: W 24 GLN cc_start: 0.8477 (pm20) cc_final: 0.8099 (pm20) REVERT: W 69 LYS cc_start: 0.8311 (tptp) cc_final: 0.7827 (ttmt) outliers start: 148 outliers final: 107 residues processed: 1038 average time/residue: 0.2255 time to fit residues: 355.0351 Evaluate side-chains 1079 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 957 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 11 THR Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 8 ASP Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 18 THR Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 5 VAL Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 18 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 THR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 67 THR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 112 optimal weight: 0.0470 chunk 120 optimal weight: 0.0970 chunk 87 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 ASN E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN N 80 GLN N 81 ASN P 40 ASN Q 40 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15019 Z= 0.213 Angle : 0.727 13.733 20470 Z= 0.360 Chirality : 0.040 0.249 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.457 50.694 2045 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 7.17 % Allowed : 31.43 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.51 (0.19), residues: 1840 helix: 3.76 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.96 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 10 PHE 0.015 0.001 PHE N 82 TYR 0.028 0.001 TYR T 50 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 961 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8187 (t70) REVERT: A 56 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8344 (mm-30) REVERT: B 50 TYR cc_start: 0.8884 (t80) cc_final: 0.8680 (t80) REVERT: C 21 ASP cc_start: 0.8543 (m-30) cc_final: 0.8079 (m-30) REVERT: C 23 THR cc_start: 0.9212 (m) cc_final: 0.8778 (p) REVERT: C 50 TYR cc_start: 0.9026 (t80) cc_final: 0.8813 (t80) REVERT: C 60 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.7774 (t80) REVERT: C 75 ASP cc_start: 0.7815 (m-30) cc_final: 0.7565 (m-30) REVERT: D 27 GLN cc_start: 0.8981 (mt0) cc_final: 0.8533 (mt0) REVERT: D 56 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8117 (mm-30) REVERT: E 27 GLN cc_start: 0.9040 (mt0) cc_final: 0.8465 (mt0) REVERT: E 42 SER cc_start: 0.9281 (m) cc_final: 0.8350 (m) REVERT: E 45 GLN cc_start: 0.8309 (tp40) cc_final: 0.7947 (tp40) REVERT: E 80 GLN cc_start: 0.9095 (tp40) cc_final: 0.8806 (tp-100) REVERT: F 45 GLN cc_start: 0.8495 (tp40) cc_final: 0.7562 (tm-30) REVERT: G 21 ASP cc_start: 0.8357 (m-30) cc_final: 0.8020 (m-30) REVERT: G 24 GLN cc_start: 0.8392 (pm20) cc_final: 0.8165 (pm20) REVERT: G 45 GLN cc_start: 0.8503 (tp40) cc_final: 0.8235 (tm-30) REVERT: G 49 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7822 (mt-10) REVERT: G 56 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8143 (mm-30) REVERT: G 59 LEU cc_start: 0.9316 (mm) cc_final: 0.9090 (mt) REVERT: G 72 LYS cc_start: 0.8868 (ttpt) cc_final: 0.7743 (ttmt) REVERT: H 20 ASP cc_start: 0.8889 (m-30) cc_final: 0.8560 (m-30) REVERT: H 23 THR cc_start: 0.9012 (m) cc_final: 0.8632 (p) REVERT: H 56 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: H 72 LYS cc_start: 0.8815 (ttpt) cc_final: 0.7724 (tttt) REVERT: I 23 THR cc_start: 0.9078 (m) cc_final: 0.8726 (p) REVERT: I 45 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8086 (tm-30) REVERT: I 56 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8432 (mm-30) REVERT: I 60 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8149 (t80) REVERT: I 72 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8031 (ttmt) REVERT: J 39 LYS cc_start: 0.9319 (mmtt) cc_final: 0.8960 (mmmt) REVERT: J 56 GLU cc_start: 0.8981 (tt0) cc_final: 0.8618 (mt-10) REVERT: J 72 LYS cc_start: 0.8892 (ttpt) cc_final: 0.7830 (ttmt) REVERT: J 80 GLN cc_start: 0.9108 (tp-100) cc_final: 0.8765 (tp40) REVERT: K 21 ASP cc_start: 0.8425 (m-30) cc_final: 0.8104 (m-30) REVERT: K 35 ASP cc_start: 0.8969 (m-30) cc_final: 0.8657 (m-30) REVERT: K 56 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8649 (mt-10) REVERT: K 60 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.7651 (t80) REVERT: K 72 LYS cc_start: 0.9035 (ttpt) cc_final: 0.7839 (ttmt) REVERT: L 40 ASN cc_start: 0.8586 (p0) cc_final: 0.8367 (p0) REVERT: L 56 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8623 (mt-10) REVERT: L 60 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.7771 (t80) REVERT: L 72 LYS cc_start: 0.8650 (ttpt) cc_final: 0.7710 (ttmt) REVERT: M 56 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8437 (mm-30) REVERT: N 14 SER cc_start: 0.8902 (t) cc_final: 0.8509 (p) REVERT: N 27 GLN cc_start: 0.8963 (mt0) cc_final: 0.8679 (mt0) REVERT: N 45 GLN cc_start: 0.8470 (tp40) cc_final: 0.8129 (tm-30) REVERT: O 21 ASP cc_start: 0.8531 (m-30) cc_final: 0.8025 (m-30) REVERT: O 24 GLN cc_start: 0.8750 (pm20) cc_final: 0.8343 (pm20) REVERT: O 45 GLN cc_start: 0.8245 (tp40) cc_final: 0.7692 (tm-30) REVERT: O 49 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7157 (mt-10) REVERT: O 56 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8584 (mt-10) REVERT: O 69 LYS cc_start: 0.8409 (tptp) cc_final: 0.8175 (tptp) REVERT: O 75 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8705 (t0) REVERT: P 27 GLN cc_start: 0.9028 (mt0) cc_final: 0.8283 (mt0) REVERT: P 35 ASP cc_start: 0.8880 (m-30) cc_final: 0.8648 (m-30) REVERT: P 80 GLN cc_start: 0.9031 (tp40) cc_final: 0.8587 (tp-100) REVERT: Q 24 GLN cc_start: 0.8316 (pm20) cc_final: 0.8085 (pm20) REVERT: Q 35 ASP cc_start: 0.8965 (m-30) cc_final: 0.8560 (m-30) REVERT: R 29 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7849 (mt-10) REVERT: S 56 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: S 69 LYS cc_start: 0.8583 (tptp) cc_final: 0.7441 (mttm) REVERT: S 72 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8805 (ttpp) REVERT: T 45 GLN cc_start: 0.8315 (tp40) cc_final: 0.7973 (tm-30) REVERT: T 60 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7682 (t80) REVERT: T 69 LYS cc_start: 0.8340 (tptp) cc_final: 0.7325 (mttt) REVERT: U 23 THR cc_start: 0.9285 (m) cc_final: 0.8637 (p) REVERT: U 27 GLN cc_start: 0.8849 (mt0) cc_final: 0.8321 (tt0) REVERT: U 45 GLN cc_start: 0.8792 (tp40) cc_final: 0.8265 (tm-30) REVERT: U 54 LEU cc_start: 0.9039 (tp) cc_final: 0.8794 (tt) REVERT: U 56 GLU cc_start: 0.8723 (tt0) cc_final: 0.8022 (mm-30) REVERT: U 69 LYS cc_start: 0.8415 (tptp) cc_final: 0.7267 (mttt) REVERT: V 14 SER cc_start: 0.8964 (t) cc_final: 0.8515 (p) REVERT: V 60 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.8357 (t80) REVERT: V 69 LYS cc_start: 0.8368 (tptp) cc_final: 0.7221 (mttm) REVERT: V 79 ILE cc_start: 0.8959 (mm) cc_final: 0.8678 (mm) REVERT: W 21 ASP cc_start: 0.8537 (m-30) cc_final: 0.8084 (m-30) REVERT: W 23 THR cc_start: 0.9314 (m) cc_final: 0.8943 (p) REVERT: W 24 GLN cc_start: 0.8620 (pm20) cc_final: 0.8263 (pm20) REVERT: W 69 LYS cc_start: 0.8251 (tptp) cc_final: 0.7797 (ttmt) outliers start: 122 outliers final: 88 residues processed: 1022 average time/residue: 0.2204 time to fit residues: 343.9921 Evaluate side-chains 1053 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 953 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 40 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain N residue 81 ASN Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 11 THR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.0570 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 80 GLN Q 40 ASN S 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15019 Z= 0.242 Angle : 0.747 14.029 20470 Z= 0.370 Chirality : 0.040 0.305 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.484 50.287 2045 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 6.87 % Allowed : 32.31 % Favored : 60.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.43 (0.19), residues: 1840 helix: 3.70 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.93 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 10 PHE 0.004 0.001 PHE R 82 TYR 0.028 0.001 TYR T 50 ARG 0.002 0.000 ARG E 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 964 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8217 (t70) REVERT: A 56 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8374 (mm-30) REVERT: C 21 ASP cc_start: 0.8536 (m-30) cc_final: 0.8096 (m-30) REVERT: C 23 THR cc_start: 0.9184 (m) cc_final: 0.8579 (p) REVERT: C 60 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7684 (t80) REVERT: D 27 GLN cc_start: 0.8980 (mt0) cc_final: 0.8534 (mt0) REVERT: E 27 GLN cc_start: 0.9069 (mt0) cc_final: 0.8487 (mp10) REVERT: E 42 SER cc_start: 0.9323 (m) cc_final: 0.8417 (m) REVERT: E 80 GLN cc_start: 0.9110 (tp40) cc_final: 0.8811 (tp-100) REVERT: F 45 GLN cc_start: 0.8523 (tp40) cc_final: 0.7597 (tm-30) REVERT: G 21 ASP cc_start: 0.8373 (m-30) cc_final: 0.8044 (m-30) REVERT: G 24 GLN cc_start: 0.8442 (pm20) cc_final: 0.8200 (pm20) REVERT: G 45 GLN cc_start: 0.8534 (tp40) cc_final: 0.8275 (tm-30) REVERT: G 49 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7865 (mt-10) REVERT: G 59 LEU cc_start: 0.9366 (mm) cc_final: 0.9152 (mt) REVERT: G 72 LYS cc_start: 0.8949 (ttpt) cc_final: 0.7847 (ttmt) REVERT: H 20 ASP cc_start: 0.8893 (m-30) cc_final: 0.8561 (m-30) REVERT: H 23 THR cc_start: 0.9014 (m) cc_final: 0.8633 (p) REVERT: H 56 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8529 (mm-30) REVERT: H 72 LYS cc_start: 0.8822 (ttpt) cc_final: 0.7811 (ttmt) REVERT: I 23 THR cc_start: 0.9081 (m) cc_final: 0.8722 (p) REVERT: I 45 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8075 (tm-30) REVERT: I 56 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8410 (mm-30) REVERT: I 60 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8215 (t80) REVERT: I 72 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8033 (ttmt) REVERT: J 39 LYS cc_start: 0.9310 (mmtt) cc_final: 0.8946 (mmmt) REVERT: J 56 GLU cc_start: 0.8999 (tt0) cc_final: 0.8627 (mt-10) REVERT: J 72 LYS cc_start: 0.8901 (ttpt) cc_final: 0.7832 (ttmt) REVERT: J 80 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8787 (tp40) REVERT: K 21 ASP cc_start: 0.8441 (m-30) cc_final: 0.8110 (m-30) REVERT: K 35 ASP cc_start: 0.8979 (m-30) cc_final: 0.8639 (m-30) REVERT: K 56 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8639 (mt-10) REVERT: K 72 LYS cc_start: 0.9044 (ttpt) cc_final: 0.7842 (ttmt) REVERT: L 40 ASN cc_start: 0.8618 (p0) cc_final: 0.8402 (p0) REVERT: L 45 GLN cc_start: 0.8709 (tp40) cc_final: 0.8411 (tp40) REVERT: L 56 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8660 (mt-10) REVERT: L 60 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.7764 (t80) REVERT: L 72 LYS cc_start: 0.8661 (ttpt) cc_final: 0.7720 (ttmt) REVERT: M 56 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8446 (mm-30) REVERT: N 27 GLN cc_start: 0.8944 (mt0) cc_final: 0.8677 (mt0) REVERT: N 56 GLU cc_start: 0.8882 (mt-10) cc_final: 0.7965 (mm-30) REVERT: N 80 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8709 (tp-100) REVERT: O 21 ASP cc_start: 0.8554 (m-30) cc_final: 0.8043 (m-30) REVERT: O 24 GLN cc_start: 0.8785 (pm20) cc_final: 0.8368 (pm20) REVERT: O 45 GLN cc_start: 0.8270 (tp40) cc_final: 0.7693 (tm-30) REVERT: O 49 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7159 (mt-10) REVERT: O 56 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8662 (mt-10) REVERT: O 69 LYS cc_start: 0.8419 (tptp) cc_final: 0.8182 (tptp) REVERT: O 75 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (t0) REVERT: P 27 GLN cc_start: 0.9042 (mt0) cc_final: 0.8318 (mt0) REVERT: P 35 ASP cc_start: 0.8846 (m-30) cc_final: 0.8588 (m-30) REVERT: P 80 GLN cc_start: 0.9045 (tp40) cc_final: 0.8599 (tp-100) REVERT: Q 24 GLN cc_start: 0.8378 (pm20) cc_final: 0.8134 (pm20) REVERT: Q 35 ASP cc_start: 0.8978 (m-30) cc_final: 0.8566 (m-30) REVERT: R 29 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7977 (mt-10) REVERT: R 32 LEU cc_start: 0.9297 (mm) cc_final: 0.9096 (mm) REVERT: S 56 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: S 69 LYS cc_start: 0.8586 (tptp) cc_final: 0.7436 (mttm) REVERT: S 72 LYS cc_start: 0.9027 (tmmt) cc_final: 0.8813 (ttpp) REVERT: T 45 GLN cc_start: 0.8339 (tp40) cc_final: 0.7982 (tm-30) REVERT: T 60 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7680 (t80) REVERT: T 69 LYS cc_start: 0.8339 (tptp) cc_final: 0.7323 (mttt) REVERT: U 23 THR cc_start: 0.9300 (m) cc_final: 0.8657 (p) REVERT: U 27 GLN cc_start: 0.8837 (mt0) cc_final: 0.8304 (tt0) REVERT: U 45 GLN cc_start: 0.8763 (tp40) cc_final: 0.8282 (tm-30) REVERT: U 54 LEU cc_start: 0.9051 (tp) cc_final: 0.8810 (tt) REVERT: U 69 LYS cc_start: 0.8418 (tptp) cc_final: 0.7265 (mttt) REVERT: V 14 SER cc_start: 0.8962 (t) cc_final: 0.8517 (p) REVERT: V 60 TYR cc_start: 0.8924 (OUTLIER) cc_final: 0.8277 (t80) REVERT: V 69 LYS cc_start: 0.8361 (tptp) cc_final: 0.7210 (mttm) REVERT: V 79 ILE cc_start: 0.8969 (mm) cc_final: 0.8697 (mm) REVERT: W 21 ASP cc_start: 0.8564 (m-30) cc_final: 0.8196 (m-30) REVERT: W 24 GLN cc_start: 0.8634 (pm20) cc_final: 0.8342 (pm20) REVERT: W 69 LYS cc_start: 0.8258 (tptp) cc_final: 0.7800 (ttmt) outliers start: 117 outliers final: 96 residues processed: 1022 average time/residue: 0.2248 time to fit residues: 349.9534 Evaluate side-chains 1063 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 956 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 15 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 11 THR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 168 optimal weight: 0.0980 chunk 145 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN F 80 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN M 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15019 Z= 0.249 Angle : 0.769 13.938 20470 Z= 0.380 Chirality : 0.040 0.336 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.513 50.293 2045 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 6.87 % Allowed : 32.55 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.35 (0.19), residues: 1840 helix: 3.63 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.91 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 10 PHE 0.007 0.001 PHE N 82 TYR 0.028 0.001 TYR T 50 ARG 0.002 0.000 ARG T 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3680 Ramachandran restraints generated. 1840 Oldfield, 0 Emsley, 1840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1072 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 955 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8181 (t70) REVERT: A 43 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7846 (t0) REVERT: A 56 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8375 (mm-30) REVERT: C 21 ASP cc_start: 0.8541 (m-30) cc_final: 0.8109 (m-30) REVERT: C 23 THR cc_start: 0.9201 (m) cc_final: 0.8628 (p) REVERT: C 50 TYR cc_start: 0.9072 (t80) cc_final: 0.8751 (t80) REVERT: C 60 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.7784 (t80) REVERT: D 27 GLN cc_start: 0.8969 (mt0) cc_final: 0.8522 (mt0) REVERT: D 75 ASP cc_start: 0.7340 (m-30) cc_final: 0.7129 (m-30) REVERT: E 27 GLN cc_start: 0.9144 (mt0) cc_final: 0.8524 (mp10) REVERT: E 42 SER cc_start: 0.9331 (m) cc_final: 0.8421 (m) REVERT: E 80 GLN cc_start: 0.9149 (tp40) cc_final: 0.8768 (tp-100) REVERT: F 45 GLN cc_start: 0.8569 (tp40) cc_final: 0.7555 (tm-30) REVERT: G 21 ASP cc_start: 0.8368 (m-30) cc_final: 0.8039 (m-30) REVERT: G 24 GLN cc_start: 0.8464 (pm20) cc_final: 0.8218 (pm20) REVERT: G 45 GLN cc_start: 0.8548 (tp40) cc_final: 0.8284 (tm-30) REVERT: G 49 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7853 (mt-10) REVERT: G 59 LEU cc_start: 0.9368 (mm) cc_final: 0.9150 (mt) REVERT: G 72 LYS cc_start: 0.8957 (ttpt) cc_final: 0.7845 (ttmt) REVERT: H 20 ASP cc_start: 0.8893 (m-30) cc_final: 0.8577 (m-30) REVERT: H 23 THR cc_start: 0.9135 (m) cc_final: 0.8720 (p) REVERT: H 45 GLN cc_start: 0.8708 (tp40) cc_final: 0.8467 (tp40) REVERT: H 56 GLU cc_start: 0.8960 (OUTLIER) cc_final: 0.8531 (mm-30) REVERT: H 72 LYS cc_start: 0.8820 (ttpt) cc_final: 0.7799 (ttmt) REVERT: H 80 GLN cc_start: 0.9054 (tp-100) cc_final: 0.8833 (tp-100) REVERT: I 23 THR cc_start: 0.9067 (m) cc_final: 0.8707 (p) REVERT: I 45 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8127 (tm-30) REVERT: I 56 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8408 (mm-30) REVERT: I 60 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8196 (t80) REVERT: I 72 LYS cc_start: 0.9005 (ttpt) cc_final: 0.8032 (ttmt) REVERT: J 18 THR cc_start: 0.8917 (m) cc_final: 0.8519 (m) REVERT: J 39 LYS cc_start: 0.9313 (mmtt) cc_final: 0.8948 (mmmt) REVERT: J 45 GLN cc_start: 0.8742 (tp40) cc_final: 0.8368 (tm-30) REVERT: J 56 GLU cc_start: 0.9034 (tt0) cc_final: 0.8655 (mt-10) REVERT: J 72 LYS cc_start: 0.8908 (ttpt) cc_final: 0.7831 (ttmt) REVERT: J 80 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8779 (tp40) REVERT: K 21 ASP cc_start: 0.8440 (m-30) cc_final: 0.8103 (m-30) REVERT: K 35 ASP cc_start: 0.8977 (m-30) cc_final: 0.8617 (m-30) REVERT: K 56 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8633 (mt-10) REVERT: K 72 LYS cc_start: 0.9041 (ttpt) cc_final: 0.7982 (ttmt) REVERT: L 40 ASN cc_start: 0.8605 (p0) cc_final: 0.8385 (p0) REVERT: L 45 GLN cc_start: 0.8733 (tp40) cc_final: 0.8058 (tp-100) REVERT: L 56 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8641 (mt-10) REVERT: L 60 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7640 (t80) REVERT: L 72 LYS cc_start: 0.8666 (ttpt) cc_final: 0.7722 (ttmt) REVERT: M 27 GLN cc_start: 0.9103 (mt0) cc_final: 0.8823 (mp10) REVERT: M 56 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8442 (mm-30) REVERT: N 27 GLN cc_start: 0.8948 (mt0) cc_final: 0.8668 (mt0) REVERT: N 56 GLU cc_start: 0.8885 (mt-10) cc_final: 0.7943 (mm-30) REVERT: N 80 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8674 (tp-100) REVERT: O 21 ASP cc_start: 0.8557 (m-30) cc_final: 0.8043 (m-30) REVERT: O 24 GLN cc_start: 0.8803 (pm20) cc_final: 0.8384 (pm20) REVERT: O 45 GLN cc_start: 0.8265 (tp40) cc_final: 0.7678 (tm-30) REVERT: O 49 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7099 (mt-10) REVERT: O 56 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8799 (mt-10) REVERT: O 69 LYS cc_start: 0.8419 (tptp) cc_final: 0.8180 (tptp) REVERT: O 75 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8695 (t0) REVERT: P 27 GLN cc_start: 0.9056 (mt0) cc_final: 0.8294 (mt0) REVERT: P 35 ASP cc_start: 0.8841 (m-30) cc_final: 0.8571 (m-30) REVERT: P 80 GLN cc_start: 0.9051 (tp40) cc_final: 0.8610 (tp-100) REVERT: Q 24 GLN cc_start: 0.8347 (pm20) cc_final: 0.8100 (pm20) REVERT: Q 35 ASP cc_start: 0.8980 (m-30) cc_final: 0.8549 (m-30) REVERT: R 80 GLN cc_start: 0.8956 (tp40) cc_final: 0.8448 (tp40) REVERT: S 56 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: S 69 LYS cc_start: 0.8591 (tptp) cc_final: 0.7512 (mttm) REVERT: S 72 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8829 (ttpp) REVERT: T 45 GLN cc_start: 0.8343 (tp40) cc_final: 0.7981 (tm-30) REVERT: T 60 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7597 (t80) REVERT: T 69 LYS cc_start: 0.8337 (tptp) cc_final: 0.7317 (mttt) REVERT: U 23 THR cc_start: 0.9310 (m) cc_final: 0.8672 (p) REVERT: U 27 GLN cc_start: 0.8861 (mt0) cc_final: 0.8310 (tt0) REVERT: U 45 GLN cc_start: 0.8798 (tp40) cc_final: 0.8409 (tm-30) REVERT: U 54 LEU cc_start: 0.9052 (tp) cc_final: 0.8813 (tt) REVERT: U 69 LYS cc_start: 0.8424 (tptp) cc_final: 0.7232 (mttt) REVERT: V 14 SER cc_start: 0.8965 (t) cc_final: 0.8518 (p) REVERT: V 60 TYR cc_start: 0.8933 (OUTLIER) cc_final: 0.8257 (t80) REVERT: V 69 LYS cc_start: 0.8364 (tptp) cc_final: 0.7211 (mttm) REVERT: W 21 ASP cc_start: 0.8556 (m-30) cc_final: 0.8159 (m-30) REVERT: W 23 THR cc_start: 0.9314 (m) cc_final: 0.8931 (p) REVERT: W 24 GLN cc_start: 0.8648 (pm20) cc_final: 0.8343 (pm20) REVERT: W 45 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8392 (tm-30) REVERT: W 69 LYS cc_start: 0.8263 (tptp) cc_final: 0.7801 (ttmt) outliers start: 117 outliers final: 95 residues processed: 1014 average time/residue: 0.2241 time to fit residues: 346.4292 Evaluate side-chains 1062 residues out of total 1702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 955 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 60 TYR Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain C residue 11 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 60 TYR Chi-restraints excluded: chain D residue 8 ASP Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain D residue 25 THR Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 11 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 60 TYR Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 60 TYR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 60 TYR Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 60 TYR Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain I residue 31 THR Chi-restraints excluded: chain I residue 60 TYR Chi-restraints excluded: chain J residue 11 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 40 ASN Chi-restraints excluded: chain J residue 60 TYR Chi-restraints excluded: chain J residue 78 ILE Chi-restraints excluded: chain K residue 11 THR Chi-restraints excluded: chain K residue 31 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 56 GLU Chi-restraints excluded: chain K residue 60 TYR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain L residue 11 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 GLU Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 34 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain N residue 18 THR Chi-restraints excluded: chain N residue 31 THR Chi-restraints excluded: chain N residue 60 TYR Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 11 THR Chi-restraints excluded: chain O residue 18 THR Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 78 ILE Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 31 THR Chi-restraints excluded: chain P residue 60 TYR Chi-restraints excluded: chain Q residue 5 VAL Chi-restraints excluded: chain Q residue 11 THR Chi-restraints excluded: chain Q residue 25 THR Chi-restraints excluded: chain Q residue 31 THR Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 60 TYR Chi-restraints excluded: chain R residue 5 VAL Chi-restraints excluded: chain R residue 11 THR Chi-restraints excluded: chain R residue 31 THR Chi-restraints excluded: chain R residue 49 GLU Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 60 TYR Chi-restraints excluded: chain S residue 11 THR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 56 GLU Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 60 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain T residue 11 THR Chi-restraints excluded: chain T residue 60 TYR Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain U residue 11 THR Chi-restraints excluded: chain U residue 18 THR Chi-restraints excluded: chain U residue 60 TYR Chi-restraints excluded: chain V residue 5 VAL Chi-restraints excluded: chain V residue 8 ASP Chi-restraints excluded: chain V residue 11 THR Chi-restraints excluded: chain V residue 18 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 60 TYR Chi-restraints excluded: chain W residue 18 THR Chi-restraints excluded: chain W residue 60 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.0970 chunk 128 optimal weight: 5.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN F 40 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN Q 40 ASN U 80 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.098611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081580 restraints weight = 26806.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085141 restraints weight = 12786.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087651 restraints weight = 7623.986| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15019 Z= 0.224 Angle : 0.768 14.066 20470 Z= 0.375 Chirality : 0.040 0.333 2461 Planarity : 0.006 0.051 2668 Dihedral : 6.479 50.081 2045 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.23 % Allowed : 32.73 % Favored : 61.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.37 (0.19), residues: 1840 helix: 3.65 (0.12), residues: 1587 sheet: None (None), residues: 0 loop : -2.86 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 10 PHE 0.005 0.001 PHE N 82 TYR 0.026 0.001 TYR T 50 ARG 0.002 0.000 ARG E 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5298.97 seconds wall clock time: 95 minutes 44.16 seconds (5744.16 seconds total)