Starting phenix.real_space_refine on Thu Feb 15 10:02:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eue_28612/02_2024/8eue_28612_neut.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.104 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 12 5.16 5 C 6592 2.51 5 N 2216 2.21 5 O 2814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 105": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 65": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "K TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11926 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 780 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 616 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 79} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 704 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3010 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 Time building chain proxies: 6.69, per 1000 atoms: 0.56 Number of scatterers: 11926 At special positions: 0 Unit cell: (116.9, 121.075, 105.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 292 15.00 O 2814 8.00 N 2216 7.00 C 6592 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: 6.94 Conformation dependent library (CDL) restraints added in 1.2 seconds 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 73.0% alpha, 1.9% beta 146 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.659A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.547A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.768A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.693A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.646A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.374A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 4.094A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.899A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.766A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 4.102A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.892A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.126A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.530A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.649A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.348A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 4.206A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.645A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.778A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 99 removed outlier: 3.595A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 16 through 22 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 45 through 72 removed outlier: 4.131A pdb=" N VAL K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 89 removed outlier: 3.626A pdb=" N LEU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.522A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.778A pdb=" N THR B 96 " --> pdb=" O THR K 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.084A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'H' and resid 85 through 86 385 hydrogen bonds defined for protein. 1140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 352 hydrogen bonds 704 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 7.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1765 1.33 - 1.45: 4768 1.45 - 1.58: 5595 1.58 - 1.70: 585 1.70 - 1.83: 22 Bond restraints: 12735 Sorted by residual: bond pdb=" CG1 ILE H 58 " pdb=" CD1 ILE H 58 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.94e+00 bond pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 1.336 1.362 -0.026 1.08e-02 8.57e+03 5.77e+00 bond pdb=" CB ILE E 51 " pdb=" CG2 ILE E 51 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.95e+00 bond pdb=" CB PHE H 67 " pdb=" CG PHE H 67 " ideal model delta sigma weight residual 1.502 1.553 -0.051 2.30e-02 1.89e+03 4.93e+00 bond pdb=" CG LEU F 62 " pdb=" CD1 LEU F 62 " ideal model delta sigma weight residual 1.521 1.448 0.073 3.30e-02 9.18e+02 4.91e+00 ... (remaining 12730 not shown) Histogram of bond angle deviations from ideal: 69.44 - 83.03: 2 83.03 - 96.61: 2 96.61 - 110.19: 5270 110.19 - 123.77: 11902 123.77 - 137.36: 1292 Bond angle restraints: 18468 Sorted by residual: angle pdb=" OP1 DG I -43 " pdb=" P DG I -43 " pdb=" OP2 DG I -43 " ideal model delta sigma weight residual 120.00 79.85 40.15 3.00e+00 1.11e-01 1.79e+02 angle pdb=" OP2 DG I -43 " pdb=" P DG I -43 " pdb=" O5' DG I -43 " ideal model delta sigma weight residual 108.00 69.44 38.56 3.00e+00 1.11e-01 1.65e+02 angle pdb=" OP1 DG I -43 " pdb=" P DG I -43 " pdb=" O5' DG I -43 " ideal model delta sigma weight residual 109.00 137.36 -28.36 3.00e+00 1.11e-01 8.93e+01 angle pdb=" O3' DA I -44 " pdb=" P DG I -43 " pdb=" OP2 DG I -43 " ideal model delta sigma weight residual 108.00 133.18 -25.18 3.00e+00 1.11e-01 7.04e+01 angle pdb=" O3' DA I -44 " pdb=" P DG I -43 " pdb=" OP1 DG I -43 " ideal model delta sigma weight residual 108.00 84.68 23.32 3.00e+00 1.11e-01 6.04e+01 ... (remaining 18463 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 4035 18.47 - 36.95: 1286 36.95 - 55.42: 1339 55.42 - 73.90: 284 73.90 - 92.37: 46 Dihedral angle restraints: 6990 sinusoidal: 4813 harmonic: 2177 Sorted by residual: dihedral pdb=" CA ILE F 50 " pdb=" C ILE F 50 " pdb=" N TYR F 51 " pdb=" CA TYR F 51 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -156.98 -23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -157.93 -22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 6987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 2028 0.141 - 0.282: 71 0.282 - 0.423: 5 0.423 - 0.564: 0 0.564 - 0.705: 1 Chirality restraints: 2105 Sorted by residual: chirality pdb=" P DG I -43 " pdb=" OP1 DG I -43 " pdb=" OP2 DG I -43 " pdb=" O5' DG I -43 " both_signs ideal model delta sigma weight residual True 2.35 1.64 0.71 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL B 70 " pdb=" CA VAL B 70 " pdb=" CG1 VAL B 70 " pdb=" CG2 VAL B 70 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 2102 not shown) Planarity restraints: 1325 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 80 " 0.016 2.00e-02 2.50e+03 3.57e-02 2.55e+01 pdb=" CG TYR D 80 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR D 80 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR D 80 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR D 80 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR D 80 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR D 80 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 80 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A 121 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.062 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO A 43 " 0.158 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.050 5.00e-02 4.00e+02 ... (remaining 1322 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2143 2.77 - 3.31: 10534 3.31 - 3.84: 25256 3.84 - 4.37: 27544 4.37 - 4.90: 38028 Nonbonded interactions: 103505 Sorted by model distance: nonbonded pdb=" OG SER H 75 " pdb=" O TYR K 39 " model vdw 2.242 2.440 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.244 2.440 nonbonded pdb=" O ARG H 76 " pdb=" NH1 ARG H 76 " model vdw 2.250 2.520 nonbonded pdb=" O LYS D 54 " pdb=" OG SER D 57 " model vdw 2.266 2.440 nonbonded pdb=" O LEU A 92 " pdb=" OG SER A 96 " model vdw 2.271 2.440 ... (remaining 103500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 41 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 84 or (resid 85 and (name N or nam \ e CA or name C or name O or name CB )) or resid 86 through 129 or (resid 130 and \ (name N or name CA or name C or name O or name CB )) or resid 131 through 135)) \ selection = (chain 'E' and resid 41 through 135) } ncs_group { reference = (chain 'B' and resid 24 through 102) selection = (chain 'F' and (resid 24 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 or (resid 46 and (name N or name CA or nam \ e C or name O or name CB )) or resid 47 through 49 or (resid 50 through 51 and ( \ name N or name CA or name C or name O or name CB )) or resid 52 through 61 or (r \ esid 62 and (name N or name CA or name C or name O or name CB )) or resid 63 thr \ ough 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 87 or (resid 88 through 89 and (name N or name CA or name C or \ name O or name CB )) or resid 90 through 102)) } ncs_group { reference = (chain 'C' and (resid 15 through 50 or (resid 51 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 114 or (resid 115 and ( \ name N or name CA or name C or name O or name CB )) or resid 116 through 118)) selection = chain 'K' } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 31 through 53 or (resid 54 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 121)) } ncs_group { reference = (chain 'I' and (resid -73 through -1 or resid 1 through 73)) selection = (chain 'J' and (resid -73 through -1 or resid 1 through 73)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 13.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.180 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 40.410 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 0.110 12735 Z= 0.387 Angle : 1.331 40.147 18468 Z= 0.678 Chirality : 0.061 0.705 2105 Planarity : 0.011 0.110 1325 Dihedral : 31.225 92.370 5584 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.00 % Allowed : 41.83 % Favored : 58.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 735 helix: -1.43 (0.19), residues: 504 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS D 79 PHE 0.018 0.002 PHE H 62 TYR 0.080 0.005 TYR D 80 ARG 0.020 0.002 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7633 (t0) cc_final: 0.6992 (m-30) REVERT: A 131 ARG cc_start: 0.7638 (mmt180) cc_final: 0.7438 (mmt180) REVERT: D 90 GLU cc_start: 0.8585 (mp0) cc_final: 0.8339 (mp0) REVERT: E 76 GLN cc_start: 0.8387 (pp30) cc_final: 0.8081 (pp30) REVERT: E 90 MET cc_start: 0.8511 (mpp) cc_final: 0.8286 (mpp) REVERT: H 60 ASN cc_start: 0.9153 (t0) cc_final: 0.8756 (t0) REVERT: H 64 ASN cc_start: 0.8489 (m-40) cc_final: 0.8069 (m110) REVERT: H 92 GLN cc_start: 0.8272 (pp30) cc_final: 0.7596 (pp30) REVERT: H 102 GLU cc_start: 0.8063 (pm20) cc_final: 0.7683 (mp0) REVERT: H 103 LEU cc_start: 0.8908 (tp) cc_final: 0.7803 (tp) REVERT: K 75 LYS cc_start: 0.8489 (tppt) cc_final: 0.8129 (tppp) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2823 time to fit residues: 106.6732 Evaluate side-chains 260 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12735 Z= 0.262 Angle : 0.896 39.209 18468 Z= 0.458 Chirality : 0.039 0.434 2105 Planarity : 0.006 0.068 1325 Dihedral : 32.982 94.779 4133 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 7.19 % Allowed : 35.62 % Favored : 57.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.29), residues: 735 helix: 0.20 (0.22), residues: 520 sheet: None (None), residues: 0 loop : -1.54 (0.37), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 79 PHE 0.020 0.002 PHE H 67 TYR 0.026 0.002 TYR F 88 ARG 0.007 0.001 ARG K 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 258 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7755 (mtm-85) REVERT: A 82 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8723 (tt) REVERT: A 83 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7148 (mpp80) REVERT: D 64 ASN cc_start: 0.8146 (p0) cc_final: 0.7839 (p0) REVERT: D 90 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8523 (mp0) REVERT: E 76 GLN cc_start: 0.8295 (pp30) cc_final: 0.7971 (pp30) REVERT: H 30 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7493 (mmm160) REVERT: H 60 ASN cc_start: 0.9161 (t0) cc_final: 0.8823 (t0) REVERT: H 64 ASN cc_start: 0.8583 (m-40) cc_final: 0.8206 (m-40) REVERT: H 92 GLN cc_start: 0.8303 (pp30) cc_final: 0.7634 (pp30) outliers start: 44 outliers final: 31 residues processed: 278 average time/residue: 0.2739 time to fit residues: 103.0141 Evaluate side-chains 272 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 83 ARG Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12735 Z= 0.217 Angle : 0.866 39.529 18468 Z= 0.438 Chirality : 0.039 0.432 2105 Planarity : 0.005 0.059 1325 Dihedral : 32.684 91.962 4133 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 7.68 % Allowed : 34.48 % Favored : 57.84 % 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: 0.26 (0.30), residues: 735 helix: 0.80 (0.22), residues: 516 sheet: None (None), residues: 0 loop : -1.21 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 79 PHE 0.011 0.002 PHE E 104 TYR 0.028 0.002 TYR F 88 ARG 0.006 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 268 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8406 (mtm110) cc_final: 0.8200 (mtm-85) REVERT: C 116 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8563 (pp) REVERT: D 83 ARG cc_start: 0.8004 (mmp80) cc_final: 0.7698 (mmp80) REVERT: E 76 GLN cc_start: 0.8268 (pp30) cc_final: 0.7908 (pp30) REVERT: H 60 ASN cc_start: 0.9115 (t0) cc_final: 0.8768 (t0) REVERT: H 64 ASN cc_start: 0.8566 (m-40) cc_final: 0.8173 (m-40) REVERT: H 76 ARG cc_start: 0.8804 (tpt90) cc_final: 0.8448 (tpt90) REVERT: H 80 TYR cc_start: 0.7815 (t80) cc_final: 0.7397 (t80) REVERT: H 92 GLN cc_start: 0.8290 (pp30) cc_final: 0.7596 (pp30) REVERT: K 29 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7921 (ttp80) outliers start: 47 outliers final: 34 residues processed: 284 average time/residue: 0.2885 time to fit residues: 109.8800 Evaluate side-chains 289 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 253 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12735 Z= 0.220 Angle : 0.867 39.594 18468 Z= 0.436 Chirality : 0.039 0.419 2105 Planarity : 0.005 0.057 1325 Dihedral : 32.611 91.017 4133 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.52 % Allowed : 36.93 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.31), residues: 735 helix: 1.03 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 79 PHE 0.010 0.001 PHE D 62 TYR 0.028 0.002 TYR F 88 ARG 0.010 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 273 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.8398 (mtm110) cc_final: 0.7850 (mtm-85) REVERT: E 76 GLN cc_start: 0.8321 (pp30) cc_final: 0.7934 (pp30) REVERT: E 105 GLU cc_start: 0.8453 (tt0) cc_final: 0.7853 (tm-30) REVERT: H 92 GLN cc_start: 0.8316 (pp30) cc_final: 0.8010 (pp30) REVERT: K 29 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.7947 (ttp80) outliers start: 46 outliers final: 35 residues processed: 289 average time/residue: 0.2890 time to fit residues: 111.5786 Evaluate side-chains 290 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12735 Z= 0.215 Angle : 0.874 39.624 18468 Z= 0.437 Chirality : 0.039 0.416 2105 Planarity : 0.005 0.058 1325 Dihedral : 32.535 89.571 4133 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 8.50 % Allowed : 36.44 % Favored : 55.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.31), residues: 735 helix: 1.19 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.08 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 79 PHE 0.008 0.001 PHE E 104 TYR 0.036 0.002 TYR F 88 ARG 0.008 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 270 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 76 GLN cc_start: 0.8365 (pp30) cc_final: 0.7959 (pp30) REVERT: E 112 ILE cc_start: 0.9330 (mp) cc_final: 0.9108 (mp) REVERT: H 92 GLN cc_start: 0.8328 (pp30) cc_final: 0.8092 (pp30) REVERT: K 29 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7890 (ttp80) outliers start: 52 outliers final: 39 residues processed: 294 average time/residue: 0.2890 time to fit residues: 112.8837 Evaluate side-chains 285 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 245 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12735 Z= 0.208 Angle : 0.880 39.637 18468 Z= 0.439 Chirality : 0.039 0.414 2105 Planarity : 0.005 0.059 1325 Dihedral : 32.446 89.356 4133 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 7.52 % Allowed : 37.75 % Favored : 54.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.30), residues: 735 helix: 1.08 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.11 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 79 PHE 0.008 0.001 PHE E 104 TYR 0.023 0.002 TYR F 88 ARG 0.009 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.6895 (mpp-170) REVERT: C 61 GLU cc_start: 0.8262 (mp0) cc_final: 0.7945 (mp0) REVERT: E 59 GLU cc_start: 0.8201 (tp30) cc_final: 0.7885 (tp30) REVERT: E 112 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9120 (mp) REVERT: H 60 ASN cc_start: 0.9134 (t0) cc_final: 0.8922 (t0) REVERT: H 64 ASN cc_start: 0.8491 (m-40) cc_final: 0.8140 (m-40) REVERT: H 80 TYR cc_start: 0.7990 (t80) cc_final: 0.7721 (t80) REVERT: H 92 GLN cc_start: 0.8264 (pp30) cc_final: 0.7659 (pp30) REVERT: K 29 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8217 (ttp80) outliers start: 46 outliers final: 35 residues processed: 284 average time/residue: 0.2864 time to fit residues: 108.6805 Evaluate side-chains 283 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 245 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12735 Z= 0.204 Angle : 0.890 39.654 18468 Z= 0.439 Chirality : 0.039 0.412 2105 Planarity : 0.005 0.057 1325 Dihedral : 32.326 89.591 4133 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 6.54 % Allowed : 39.87 % Favored : 53.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.31), residues: 735 helix: 1.14 (0.22), residues: 525 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS D 79 PHE 0.010 0.001 PHE A 67 TYR 0.031 0.002 TYR F 88 ARG 0.009 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 265 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 39 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6895 (mpp-170) REVERT: E 112 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9100 (mp) REVERT: F 40 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8774 (ttt180) REVERT: H 60 ASN cc_start: 0.9115 (t0) cc_final: 0.8815 (t0) REVERT: H 64 ASN cc_start: 0.8484 (m-40) cc_final: 0.8061 (m110) REVERT: H 92 GLN cc_start: 0.8218 (pp30) cc_final: 0.7647 (pp30) REVERT: K 29 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8198 (ttp80) outliers start: 40 outliers final: 31 residues processed: 288 average time/residue: 0.2896 time to fit residues: 111.4669 Evaluate side-chains 280 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12735 Z= 0.217 Angle : 0.903 39.675 18468 Z= 0.447 Chirality : 0.039 0.404 2105 Planarity : 0.005 0.061 1325 Dihedral : 32.294 89.366 4133 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.70 % Allowed : 39.71 % Favored : 53.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.31), residues: 735 helix: 1.22 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 79 PHE 0.010 0.001 PHE C 25 TYR 0.038 0.002 TYR F 88 ARG 0.009 0.001 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8498 (tt) REVERT: B 39 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.6892 (mpp-170) REVERT: E 112 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9108 (mp) REVERT: H 60 ASN cc_start: 0.9145 (t0) cc_final: 0.8754 (t0) REVERT: H 64 ASN cc_start: 0.8560 (m-40) cc_final: 0.8063 (m-40) REVERT: H 92 GLN cc_start: 0.8272 (pp30) cc_final: 0.7561 (pp30) REVERT: K 29 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8220 (ttp80) REVERT: K 75 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8644 (mmtp) outliers start: 41 outliers final: 33 residues processed: 271 average time/residue: 0.2717 time to fit residues: 99.5873 Evaluate side-chains 274 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 18 SER Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12735 Z= 0.217 Angle : 0.914 39.685 18468 Z= 0.449 Chirality : 0.039 0.401 2105 Planarity : 0.005 0.059 1325 Dihedral : 32.234 89.292 4133 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.37 % Allowed : 39.87 % Favored : 53.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.31), residues: 735 helix: 1.19 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 79 PHE 0.009 0.001 PHE E 104 TYR 0.040 0.002 TYR F 88 ARG 0.012 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 254 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8413 (tt) REVERT: B 39 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.6897 (mpp-170) REVERT: E 112 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9080 (mp) REVERT: E 134 ARG cc_start: 0.8365 (ttm170) cc_final: 0.8084 (tmm-80) REVERT: H 64 ASN cc_start: 0.8618 (m-40) cc_final: 0.8277 (m-40) REVERT: H 92 GLN cc_start: 0.8230 (pp30) cc_final: 0.7657 (pp30) REVERT: K 29 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7806 (ttp80) outliers start: 39 outliers final: 32 residues processed: 273 average time/residue: 0.2937 time to fit residues: 107.7545 Evaluate side-chains 280 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 244 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12735 Z= 0.213 Angle : 0.920 39.693 18468 Z= 0.451 Chirality : 0.039 0.400 2105 Planarity : 0.005 0.062 1325 Dihedral : 32.159 89.704 4133 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.88 % Allowed : 41.01 % Favored : 53.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.31), residues: 735 helix: 1.22 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS D 79 PHE 0.009 0.001 PHE C 25 TYR 0.041 0.002 TYR F 88 ARG 0.012 0.001 ARG F 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1470 Ramachandran restraints generated. 735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 39 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.6884 (mpp-170) REVERT: E 112 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9069 (mp) REVERT: F 40 ARG cc_start: 0.8940 (ttm170) cc_final: 0.8733 (ttt180) REVERT: H 64 ASN cc_start: 0.8541 (m-40) cc_final: 0.8268 (m-40) REVERT: H 92 GLN cc_start: 0.8253 (pp30) cc_final: 0.7658 (pp30) REVERT: K 29 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: K 75 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8403 (mmmm) outliers start: 36 outliers final: 30 residues processed: 267 average time/residue: 0.2885 time to fit residues: 103.1867 Evaluate side-chains 272 residues out of total 625 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 64 ASN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain K residue 27 VAL Chi-restraints excluded: chain K residue 29 ARG Chi-restraints excluded: chain K residue 62 ILE Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain K residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 79 HIS F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.080356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065070 restraints weight = 54311.846| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.03 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12735 Z= 0.223 Angle : 0.928 39.711 18468 Z= 0.455 Chirality : 0.039 0.395 2105 Planarity : 0.005 0.064 1325 Dihedral : 32.153 89.463 4133 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.39 % Allowed : 41.99 % Favored : 52.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.31), residues: 735 helix: 1.21 (0.23), residues: 526 sheet: None (None), residues: 0 loop : -1.13 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 79 PHE 0.010 0.001 PHE E 104 TYR 0.039 0.002 TYR F 88 ARG 0.013 0.001 ARG F 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.24 seconds wall clock time: 52 minutes 25.97 seconds (3145.97 seconds total)