Starting phenix.real_space_refine on Sat Jul 20 20:22:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yov_10864/07_2024/6yov_10864.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.044 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 261 5.49 5 S 19 5.16 5 C 6892 2.51 5 N 2327 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12298 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2662 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "J" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2706 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain: "K" Number of atoms: 272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 272 Classifications: {'peptide': 68} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 625 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.58, per 1000 atoms: 0.62 Number of scatterers: 12298 At special positions: 0 Unit cell: (104.06, 116.96, 129.86, 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 19 16.00 P 261 15.00 O 2799 8.00 N 2327 7.00 C 6892 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=16, symmetry=0 Number of additional bonds: simple=16, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.03 Conformation dependent library (CDL) restraints added in 1.3 seconds 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1550 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 10 sheets defined 72.0% alpha, 2.7% beta 129 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.511A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 removed outlier: 3.504A pdb=" N ILE E 125 " --> pdb=" O MET E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.247A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.961A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 160 Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 180 through 189 Processing helix chain 'K' and resid 193 through 208 Proline residue: K 202 - end of helix Processing helix chain 'L' and resid 46 through 61 removed outlier: 3.566A pdb=" N GLY L 54 " --> pdb=" O VAL L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 81 Processing helix chain 'L' and resid 83 through 105 Proline residue: L 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.769A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.880A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 removed outlier: 6.800A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.855A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.218A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 477 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 330 hydrogen bonds 660 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2001 1.32 - 1.45: 4464 1.45 - 1.57: 6014 1.57 - 1.69: 522 1.69 - 1.81: 34 Bond restraints: 13035 Sorted by residual: bond pdb=" CA ASN F 26 " pdb=" C ASN F 26 " ideal model delta sigma weight residual 1.522 1.601 -0.079 1.37e-02 5.33e+03 3.32e+01 bond pdb=" O3' DT J 84 " pdb=" P DG J 85 " ideal model delta sigma weight residual 1.607 1.660 -0.053 1.50e-02 4.44e+03 1.23e+01 bond pdb=" CD ARG B 40 " pdb=" NE ARG B 40 " ideal model delta sigma weight residual 1.458 1.413 0.045 1.40e-02 5.10e+03 1.04e+01 bond pdb=" N ILE B 47 " pdb=" CA ILE B 47 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.17e-02 7.31e+03 9.88e+00 bond pdb=" NE ARG B 24 " pdb=" CZ ARG B 24 " ideal model delta sigma weight residual 1.326 1.360 -0.034 1.10e-02 8.26e+03 9.81e+00 ... (remaining 13030 not shown) Histogram of bond angle deviations from ideal: 98.22 - 105.35: 1263 105.35 - 112.48: 7071 112.48 - 119.61: 3818 119.61 - 126.74: 5842 126.74 - 133.86: 667 Bond angle restraints: 18661 Sorted by residual: angle pdb=" N LYS L 42 " pdb=" CA LYS L 42 " pdb=" C LYS L 42 " ideal model delta sigma weight residual 110.53 120.03 -9.50 1.29e+00 6.01e-01 5.43e+01 angle pdb=" C HIS L 105 " pdb=" N PRO L 106 " pdb=" CA PRO L 106 " ideal model delta sigma weight residual 119.47 127.73 -8.26 1.16e+00 7.43e-01 5.07e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 126.55 -6.99 1.02e+00 9.61e-01 4.70e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 126.48 -6.92 1.02e+00 9.61e-01 4.61e+01 angle pdb=" C LEU H 103 " pdb=" N PRO H 104 " pdb=" CA PRO H 104 " ideal model delta sigma weight residual 120.31 126.68 -6.37 9.80e-01 1.04e+00 4.23e+01 ... (remaining 18656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5050 17.90 - 35.81: 948 35.81 - 53.71: 831 53.71 - 71.61: 260 71.61 - 89.52: 12 Dihedral angle restraints: 7101 sinusoidal: 4631 harmonic: 2470 Sorted by residual: dihedral pdb=" CA PRO D 104 " pdb=" C PRO D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual 180.00 156.68 23.32 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PRO H 104 " pdb=" C PRO H 104 " pdb=" N GLY H 105 " pdb=" CA GLY H 105 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C ASN F 26 " pdb=" N ASN F 26 " pdb=" CA ASN F 26 " pdb=" CB ASN F 26 " ideal model delta harmonic sigma weight residual -122.60 -131.46 8.86 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1339 0.060 - 0.120: 573 0.120 - 0.180: 133 0.180 - 0.240: 17 0.240 - 0.300: 5 Chirality restraints: 2067 Sorted by residual: chirality pdb=" CA GLN L 61 " pdb=" N GLN L 61 " pdb=" C GLN L 61 " pdb=" CB GLN L 61 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA LEU E 66 " pdb=" N LEU E 66 " pdb=" C LEU E 66 " pdb=" CB LEU E 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ARG L 88 " pdb=" N ARG L 88 " pdb=" C ARG L 88 " pdb=" CB ARG L 88 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 2064 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 55 " 0.074 2.00e-02 2.50e+03 4.04e-02 3.27e+01 pdb=" CG TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 55 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 55 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 55 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 55 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 55 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 55 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 41 " 0.072 2.00e-02 2.50e+03 3.77e-02 2.84e+01 pdb=" CG TYR H 41 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR H 41 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR H 41 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR H 41 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR H 41 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR H 41 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 41 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 55 " -0.064 2.00e-02 2.50e+03 3.32e-02 2.20e+01 pdb=" CG TYR E 55 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR E 55 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR E 55 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR E 55 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 55 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR E 55 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 55 " -0.045 2.00e-02 2.50e+03 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 4200 2.90 - 3.40: 10733 3.40 - 3.90: 24145 3.90 - 4.40: 28333 4.40 - 4.90: 37125 Nonbonded interactions: 104536 Sorted by model distance: nonbonded pdb=" N GLU G 42 " pdb=" OE1 GLU G 42 " model vdw 2.395 2.520 nonbonded pdb=" O2 DT I 125 " pdb=" OG SER L 72 " model vdw 2.399 2.440 nonbonded pdb=" OG SER G 19 " pdb=" O PHE G 26 " model vdw 2.404 2.440 nonbonded pdb=" OG1 THR C 77 " pdb=" OP1 DG J 133 " model vdw 2.407 2.440 nonbonded pdb=" NH2 ARG A 54 " pdb=" OH TYR A 55 " model vdw 2.462 2.520 ... (remaining 104531 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 23 through 102 or resid 201)) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 9 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 34 through 125 or resid 201)) selection = (chain 'H' and (resid 34 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 201)) } 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=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 40.120 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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 : 0.011 0.091 13035 Z= 0.703 Angle : 1.137 9.504 18661 Z= 0.776 Chirality : 0.067 0.300 2067 Planarity : 0.009 0.046 1480 Dihedral : 25.194 89.518 5551 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.25), residues: 878 helix: 0.78 (0.18), residues: 650 sheet: None (None), residues: 0 loop : 0.34 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.007 TRP L 79 HIS 0.010 0.002 HIS D 110 PHE 0.046 0.010 PHE D 71 TYR 0.074 0.010 TYR A 55 ARG 0.010 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.8372 (m-30) cc_final: 0.8108 (m-30) REVERT: A 121 MET cc_start: 0.8920 (mmm) cc_final: 0.8655 (mmm) REVERT: A 124 ASP cc_start: 0.8083 (m-30) cc_final: 0.7841 (m-30) REVERT: C 26 PHE cc_start: 0.8846 (m-10) cc_final: 0.8641 (m-80) REVERT: C 40 TYR cc_start: 0.8856 (m-80) cc_final: 0.8583 (m-80) REVERT: C 102 THR cc_start: 0.8545 (m) cc_final: 0.8342 (p) REVERT: D 72 GLU cc_start: 0.8602 (tt0) cc_final: 0.8346 (tp30) REVERT: E 94 GLN cc_start: 0.9044 (tt0) cc_final: 0.8801 (tt0) REVERT: E 120 ILE cc_start: 0.9443 (mm) cc_final: 0.9156 (mt) REVERT: G 74 ASN cc_start: 0.9213 (m-40) cc_final: 0.8900 (t0) REVERT: G 102 THR cc_start: 0.8998 (m) cc_final: 0.8769 (p) REVERT: H 52 ASP cc_start: 0.8663 (p0) cc_final: 0.8433 (p0) REVERT: H 106 GLU cc_start: 0.9336 (mm-30) cc_final: 0.9135 (tt0) REVERT: H 114 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2254 time to fit residues: 113.3245 Evaluate side-chains 250 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13035 Z= 0.256 Angle : 0.650 10.383 18661 Z= 0.375 Chirality : 0.037 0.162 2067 Planarity : 0.005 0.054 1480 Dihedral : 28.407 73.763 3881 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.19 % Allowed : 18.35 % Favored : 77.46 % 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: 2.67 (0.27), residues: 878 helix: 2.30 (0.20), residues: 664 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.011 0.002 HIS B 76 PHE 0.027 0.002 PHE B 62 TYR 0.023 0.002 TYR H 41 ARG 0.007 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 282 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 51 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8462 (mm-30) REVERT: E 91 MET cc_start: 0.8863 (mmm) cc_final: 0.8579 (mmt) REVERT: E 121 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8713 (mmm) REVERT: F 27 ILE cc_start: 0.9452 (tp) cc_final: 0.9228 (tp) REVERT: G 40 TYR cc_start: 0.8667 (m-80) cc_final: 0.8426 (m-80) REVERT: G 57 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8945 (tt0) REVERT: G 102 THR cc_start: 0.9120 (m) cc_final: 0.8821 (p) outliers start: 29 outliers final: 18 residues processed: 294 average time/residue: 0.2345 time to fit residues: 97.7770 Evaluate side-chains 255 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 236 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 80 LYS Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 0.0770 chunk 102 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN G 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13035 Z= 0.272 Angle : 0.616 9.924 18661 Z= 0.360 Chirality : 0.037 0.160 2067 Planarity : 0.005 0.050 1480 Dihedral : 28.583 73.891 3881 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 5.35 % Allowed : 22.83 % Favored : 71.82 % 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: 2.63 (0.28), residues: 878 helix: 2.32 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP L 79 HIS 0.007 0.001 HIS L 101 PHE 0.016 0.002 PHE E 79 TYR 0.022 0.002 TYR B 89 ARG 0.013 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 250 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 LEU cc_start: 0.9324 (mm) cc_final: 0.9005 (mm) REVERT: C 90 ASN cc_start: 0.7514 (m-40) cc_final: 0.7160 (m-40) REVERT: D 48 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8929 (tm-30) REVERT: E 91 MET cc_start: 0.8896 (mmm) cc_final: 0.8677 (mmt) REVERT: E 121 MET cc_start: 0.8853 (mmp) cc_final: 0.8535 (mmm) REVERT: E 124 ASP cc_start: 0.8196 (m-30) cc_final: 0.7696 (m-30) REVERT: G 73 ASP cc_start: 0.8464 (m-30) cc_final: 0.8225 (m-30) REVERT: G 85 GLN cc_start: 0.9037 (tp-100) cc_final: 0.8575 (tp-100) REVERT: G 102 THR cc_start: 0.9256 (m) cc_final: 0.8978 (p) REVERT: G 105 GLN cc_start: 0.9325 (mp10) cc_final: 0.8964 (mp10) REVERT: H 106 GLU cc_start: 0.9377 (mp0) cc_final: 0.9172 (tt0) outliers start: 37 outliers final: 22 residues processed: 265 average time/residue: 0.2266 time to fit residues: 86.4510 Evaluate side-chains 248 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 43 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 103 optimal weight: 50.0000 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN F 26 ASN G 25 GLN H 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13035 Z= 0.317 Angle : 0.638 9.906 18661 Z= 0.370 Chirality : 0.038 0.168 2067 Planarity : 0.005 0.053 1480 Dihedral : 28.528 73.877 3881 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 6.21 % Allowed : 22.83 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.28), residues: 878 helix: 2.21 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -0.22 (0.38), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 51 HIS 0.004 0.001 HIS L 101 PHE 0.024 0.002 PHE D 71 TYR 0.020 0.002 TYR D 84 ARG 0.004 0.001 ARG L 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 231 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 THR cc_start: 0.9339 (m) cc_final: 0.9116 (p) REVERT: D 48 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8878 (tm-30) REVERT: D 116 THR cc_start: 0.9383 (OUTLIER) cc_final: 0.9131 (p) REVERT: E 124 ASP cc_start: 0.8187 (m-30) cc_final: 0.7930 (m-30) REVERT: F 26 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7502 (t0) REVERT: G 105 GLN cc_start: 0.9366 (mp10) cc_final: 0.9023 (mp10) outliers start: 43 outliers final: 28 residues processed: 254 average time/residue: 0.2217 time to fit residues: 80.8913 Evaluate side-chains 244 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 214 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 113 ILE Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 27 optimal weight: 50.0000 chunk 36 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 25 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS H 110 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 13035 Z= 0.395 Angle : 0.687 12.406 18661 Z= 0.393 Chirality : 0.040 0.177 2067 Planarity : 0.005 0.051 1480 Dihedral : 28.689 74.480 3881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 6.79 % Allowed : 23.12 % Favored : 70.09 % 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: 2.19 (0.28), residues: 878 helix: 2.05 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 79 HIS 0.007 0.002 HIS L 101 PHE 0.009 0.002 PHE F 62 TYR 0.027 0.002 TYR B 89 ARG 0.010 0.001 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8663 (mmm) cc_final: 0.8061 (tpp) REVERT: C 116 LEU cc_start: 0.8092 (mm) cc_final: 0.7787 (mm) REVERT: D 48 GLN cc_start: 0.9388 (tm-30) cc_final: 0.8952 (tm-30) REVERT: D 116 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9254 (p) REVERT: E 124 ASP cc_start: 0.8280 (m-30) cc_final: 0.7999 (m-30) REVERT: F 26 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7474 (t0) REVERT: G 95 ASN cc_start: 0.9298 (t0) cc_final: 0.9009 (m-40) outliers start: 47 outliers final: 36 residues processed: 244 average time/residue: 0.2150 time to fit residues: 75.4718 Evaluate side-chains 242 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 26 ASN Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.0470 chunk 105 optimal weight: 8.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13035 Z= 0.214 Angle : 0.625 12.769 18661 Z= 0.358 Chirality : 0.036 0.190 2067 Planarity : 0.004 0.051 1480 Dihedral : 28.556 74.119 3881 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.34 % Allowed : 27.60 % Favored : 68.06 % 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: 2.27 (0.28), residues: 878 helix: 2.07 (0.21), residues: 658 sheet: None (None), residues: 0 loop : -0.19 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP L 79 HIS 0.006 0.001 HIS B 76 PHE 0.014 0.001 PHE L 90 TYR 0.016 0.002 TYR B 89 ARG 0.006 0.000 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 229 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8773 (mmm) cc_final: 0.8536 (mmt) REVERT: B 81 THR cc_start: 0.9354 (m) cc_final: 0.9148 (p) REVERT: B 89 TYR cc_start: 0.8118 (m-80) cc_final: 0.7764 (m-80) REVERT: D 48 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8875 (tm-30) REVERT: D 116 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9178 (p) REVERT: G 95 ASN cc_start: 0.9223 (t0) cc_final: 0.8906 (m-40) outliers start: 30 outliers final: 22 residues processed: 247 average time/residue: 0.2290 time to fit residues: 81.0968 Evaluate side-chains 237 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 214 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13035 Z= 0.186 Angle : 0.624 11.851 18661 Z= 0.354 Chirality : 0.036 0.214 2067 Planarity : 0.004 0.051 1480 Dihedral : 28.388 74.757 3881 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.61 % Allowed : 29.05 % Favored : 67.34 % 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: 2.14 (0.28), residues: 878 helix: 1.97 (0.20), residues: 657 sheet: None (None), residues: 0 loop : -0.18 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP L 79 HIS 0.005 0.001 HIS B 76 PHE 0.014 0.001 PHE E 79 TYR 0.015 0.001 TYR H 38 ARG 0.007 0.000 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.7791 (m-80) cc_final: 0.7376 (m-80) REVERT: D 48 GLN cc_start: 0.9210 (tm-30) cc_final: 0.8862 (tm-30) REVERT: D 60 MET cc_start: 0.9320 (tpp) cc_final: 0.9068 (tpp) REVERT: G 95 ASN cc_start: 0.9177 (t0) cc_final: 0.8863 (m-40) outliers start: 25 outliers final: 18 residues processed: 248 average time/residue: 0.2249 time to fit residues: 81.1744 Evaluate side-chains 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 53 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS A 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.6345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13035 Z= 0.297 Angle : 0.661 12.642 18661 Z= 0.374 Chirality : 0.038 0.196 2067 Planarity : 0.005 0.082 1480 Dihedral : 28.437 74.433 3881 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.77 % Allowed : 29.05 % Favored : 66.18 % 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: 2.07 (0.28), residues: 878 helix: 1.89 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -0.18 (0.40), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP L 79 HIS 0.005 0.001 HIS B 76 PHE 0.023 0.002 PHE D 71 TYR 0.018 0.002 TYR F 89 ARG 0.007 0.000 ARG L 57 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.7989 (m-80) cc_final: 0.7573 (m-80) REVERT: D 48 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8927 (tm-30) REVERT: D 116 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9254 (p) REVERT: E 51 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8450 (tp30) REVERT: G 95 ASN cc_start: 0.9215 (t0) cc_final: 0.8881 (m-40) REVERT: H 103 LEU cc_start: 0.9082 (mt) cc_final: 0.8880 (tp) outliers start: 33 outliers final: 28 residues processed: 235 average time/residue: 0.2237 time to fit residues: 76.1308 Evaluate side-chains 235 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 205 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 0.0270 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN G 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13035 Z= 0.331 Angle : 0.715 20.159 18661 Z= 0.395 Chirality : 0.039 0.209 2067 Planarity : 0.005 0.082 1480 Dihedral : 28.509 74.276 3881 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.62 % Allowed : 30.64 % Favored : 64.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.28), residues: 878 helix: 1.85 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 79 HIS 0.005 0.001 HIS B 76 PHE 0.009 0.002 PHE L 48 TYR 0.021 0.002 TYR F 89 ARG 0.006 0.000 ARG L 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 213 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8780 (mmm) cc_final: 0.8547 (mmt) REVERT: B 89 TYR cc_start: 0.7990 (m-80) cc_final: 0.7534 (m-80) REVERT: D 48 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8935 (tm-30) REVERT: D 116 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9270 (p) REVERT: E 51 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8457 (tp30) REVERT: E 124 ASP cc_start: 0.8341 (m-30) cc_final: 0.8134 (m-30) REVERT: G 95 ASN cc_start: 0.9257 (t0) cc_final: 0.8936 (m-40) outliers start: 32 outliers final: 28 residues processed: 232 average time/residue: 0.2297 time to fit residues: 78.2035 Evaluate side-chains 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 202 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain L residue 66 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.9990 chunk 74 optimal weight: 40.0000 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 27 optimal weight: 0.0070 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS G 69 ASN ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13035 Z= 0.222 Angle : 0.676 14.126 18661 Z= 0.376 Chirality : 0.037 0.219 2067 Planarity : 0.005 0.085 1480 Dihedral : 28.439 74.286 3881 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.32 % Allowed : 31.36 % Favored : 65.32 % 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: 1.96 (0.29), residues: 878 helix: 1.84 (0.21), residues: 661 sheet: None (None), residues: 0 loop : -0.30 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP L 79 HIS 0.003 0.001 HIS L 101 PHE 0.009 0.001 PHE E 68 TYR 0.015 0.002 TYR G 40 ARG 0.006 0.000 ARG L 43 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1756 Ramachandran restraints generated. 878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 216 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 TYR cc_start: 0.7733 (m-80) cc_final: 0.7165 (m-80) REVERT: D 48 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8929 (tm-30) REVERT: D 116 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9237 (p) REVERT: E 78 ASP cc_start: 0.8432 (p0) cc_final: 0.8164 (p0) REVERT: G 95 ASN cc_start: 0.9240 (t0) cc_final: 0.8875 (m-40) outliers start: 23 outliers final: 21 residues processed: 229 average time/residue: 0.2288 time to fit residues: 75.6903 Evaluate side-chains 232 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 210 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain H residue 39 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN G 69 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.080054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.061357 restraints weight = 91135.350| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.07 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13035 Z= 0.320 Angle : 0.716 13.734 18661 Z= 0.398 Chirality : 0.039 0.206 2067 Planarity : 0.005 0.086 1480 Dihedral : 28.483 74.696 3881 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.90 % Allowed : 31.07 % Favored : 65.03 % 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: 2.02 (0.29), residues: 878 helix: 1.88 (0.21), residues: 657 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP L 79 HIS 0.004 0.001 HIS G 32 PHE 0.013 0.002 PHE E 68 TYR 0.022 0.002 TYR F 89 ARG 0.007 0.000 ARG G 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.58 seconds wall clock time: 43 minutes 31.97 seconds (2611.97 seconds total)