Starting phenix.real_space_refine on Sat Feb 17 21:06:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/02_2024/8upf_42446.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 32 5.16 5 C 7901 2.51 5 N 2612 2.21 5 O 3172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K GLU 25": "OE1" <-> "OE2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14012 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" 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: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1175 Classifications: {'peptide': 148} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 846 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10623 SG CYS K 31 73.925 71.146 46.276 1.00186.03 S ATOM 10773 SG CYS K 51 75.294 73.936 47.616 1.00186.41 S ATOM 10797 SG CYS K 54 74.227 74.593 43.507 1.00191.01 S ATOM 10514 SG CYS K 16 82.497 72.048 55.513 1.00233.53 S ATOM 10532 SG CYS K 19 84.522 73.207 59.045 1.00237.17 S ATOM 10662 SG CYS K 36 81.475 70.277 59.358 1.00213.12 S ATOM 10684 SG CYS K 39 81.052 73.736 58.594 1.00206.20 S Time building chain proxies: 8.31, per 1000 atoms: 0.59 Number of scatterers: 14012 At special positions: 0 Unit cell: (105.843, 127.422, 116.119, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 293 15.00 O 3172 8.00 N 2612 7.00 C 7901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1896 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 64.8% alpha, 4.3% beta 135 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.575A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.872A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.519A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.679A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.828A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.575A 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 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.916A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.802A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.544A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 46 Processing helix chain 'K' and resid 58 through 67 Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 93 removed outlier: 3.630A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid -1 through 16 Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.666A pdb=" N VAL L 102 " --> pdb=" O THR L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.544A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.568A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.708A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.456A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.237A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.629A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.411A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.590A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 481 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 7.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3005 1.33 - 1.45: 4434 1.45 - 1.57: 6805 1.57 - 1.69: 584 1.69 - 1.81: 46 Bond restraints: 14874 Sorted by residual: bond pdb=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.72e-02 3.38e+03 3.68e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.459 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" C4' DG I 9 " pdb=" C3' DG I 9 " ideal model delta sigma weight residual 1.523 1.500 0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 14869 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.04: 1291 105.04 - 112.28: 8359 112.28 - 119.52: 4546 119.52 - 126.77: 6296 126.77 - 134.01: 866 Bond angle restraints: 21358 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 122.46 126.18 -3.72 1.41e+00 5.03e-01 6.96e+00 angle pdb=" C3' DT J 66 " pdb=" C2' DT J 66 " pdb=" C1' DT J 66 " ideal model delta sigma weight residual 101.60 97.80 3.80 1.50e+00 4.44e-01 6.43e+00 angle pdb=" C3' DT J -29 " pdb=" C2' DT J -29 " pdb=" C1' DT J -29 " ideal model delta sigma weight residual 101.60 97.87 3.73 1.50e+00 4.44e-01 6.19e+00 angle pdb=" N LYS E 37 " pdb=" CA LYS E 37 " pdb=" C LYS E 37 " ideal model delta sigma weight residual 111.00 117.52 -6.52 2.80e+00 1.28e-01 5.42e+00 angle pdb=" N LYS A 37 " pdb=" CA LYS A 37 " pdb=" C LYS A 37 " ideal model delta sigma weight residual 111.00 117.51 -6.51 2.80e+00 1.28e-01 5.41e+00 ... (remaining 21353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 6568 31.32 - 62.63: 1617 62.63 - 93.95: 46 93.95 - 125.27: 0 125.27 - 156.58: 2 Dihedral angle restraints: 8233 sinusoidal: 5297 harmonic: 2936 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 63.42 156.58 1 3.50e+01 8.16e-04 1.50e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 65.18 154.82 1 3.50e+01 8.16e-04 1.49e+01 dihedral pdb=" CA HIS H 49 " pdb=" C HIS H 49 " pdb=" N PRO H 50 " pdb=" CA PRO H 50 " ideal model delta harmonic sigma weight residual -180.00 -162.73 -17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 8230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1533 0.033 - 0.067: 702 0.067 - 0.100: 133 0.100 - 0.133: 44 0.133 - 0.167: 8 Chirality restraints: 2420 Sorted by residual: chirality pdb=" CA LYS E 37 " pdb=" N LYS E 37 " pdb=" C LYS E 37 " pdb=" CB LYS E 37 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA LYS A 37 " pdb=" N LYS A 37 " pdb=" C LYS A 37 " pdb=" CB LYS A 37 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 2417 not shown) Planarity restraints: 1691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.029 2.00e-02 2.50e+03 1.19e-02 4.28e+00 pdb=" N9 DG I 47 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -5 " -0.028 2.00e-02 2.50e+03 1.24e-02 4.22e+00 pdb=" N9 DA I -5 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -5 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I -5 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DA I -5 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -5 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -5 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -5 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -5 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -5 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -5 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.031 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO B 32 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.026 5.00e-02 4.00e+02 ... (remaining 1688 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 2292 2.76 - 3.47: 19473 3.47 - 4.19: 38753 4.19 - 4.90: 60050 Nonbonded interactions: 120570 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.329 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.065 2.496 nonbonded pdb=" OG SER D 78 " pdb=" O TYR C 39 " model vdw 2.141 2.440 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.163 2.440 ... (remaining 120565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 4.380 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 48.370 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 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 0.041 14874 Z= 0.410 Angle : 0.650 6.516 21358 Z= 0.387 Chirality : 0.039 0.167 2420 Planarity : 0.004 0.046 1691 Dihedral : 26.919 156.584 6337 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.47 % Allowed : 5.00 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.24 (0.24), residues: 989 helix: -0.85 (0.18), residues: 647 sheet: -1.85 (0.94), residues: 23 loop : -2.60 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 61 HIS 0.004 0.001 HIS L 75 PHE 0.011 0.001 PHE E 78 TYR 0.013 0.002 TYR C 50 ARG 0.003 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9188 (m-80) cc_final: 0.8895 (m-80) REVERT: A 59 GLU cc_start: 0.8466 (pm20) cc_final: 0.8160 (pm20) REVERT: A 60 LEU cc_start: 0.9166 (mt) cc_final: 0.8852 (mt) REVERT: A 80 THR cc_start: 0.8601 (t) cc_final: 0.8045 (t) REVERT: B 92 ARG cc_start: 0.8680 (ttp80) cc_final: 0.8347 (ttp80) REVERT: D 59 MET cc_start: 0.8950 (tpp) cc_final: 0.7857 (tpt) REVERT: D 83 TYR cc_start: 0.8630 (m-10) cc_final: 0.8335 (m-10) REVERT: D 108 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7484 (mtpp) REVERT: E 50 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7417 (mt-10) REVERT: F 25 ASN cc_start: 0.8460 (m110) cc_final: 0.7918 (m-40) REVERT: F 91 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8768 (ttpp) REVERT: H 86 ARG cc_start: 0.8808 (mmt-90) cc_final: 0.8579 (ttm-80) REVERT: H 113 GLU cc_start: 0.8517 (tp30) cc_final: 0.8249 (tm-30) REVERT: H 120 LYS cc_start: 0.8475 (tttm) cc_final: 0.8222 (tttt) REVERT: K 20 MET cc_start: 0.7240 (mmp) cc_final: 0.6847 (mpp) REVERT: L 30 MET cc_start: 0.6403 (ptt) cc_final: 0.6106 (mmm) REVERT: C 104 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8731 (tp40) REVERT: G 36 LYS cc_start: 0.8543 (pttt) cc_final: 0.8029 (mmmm) REVERT: G 104 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8464 (mm-40) outliers start: 4 outliers final: 0 residues processed: 176 average time/residue: 0.4220 time to fit residues: 95.0801 Evaluate side-chains 156 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 40.0000 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN F 93 GLN K 41 GLN K 81 GLN K 83 HIS L 77 ASN C 112 GLN G 38 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14874 Z= 0.248 Angle : 0.580 5.949 21358 Z= 0.336 Chirality : 0.036 0.144 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.719 156.621 4324 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 10.70 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -0.09 (0.26), residues: 989 helix: 0.86 (0.20), residues: 656 sheet: -1.00 (1.08), residues: 23 loop : -1.96 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.010 0.002 PHE L 62 TYR 0.023 0.002 TYR H 121 ARG 0.005 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8305 (pm20) cc_final: 0.8077 (pm20) REVERT: B 84 MET cc_start: 0.8541 (mmm) cc_final: 0.8084 (mmm) REVERT: B 92 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8489 (ttp80) REVERT: D 47 GLN cc_start: 0.8648 (mt0) cc_final: 0.8446 (tt0) REVERT: D 68 ASP cc_start: 0.8936 (t70) cc_final: 0.8633 (t0) REVERT: D 108 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7405 (mtpp) REVERT: F 25 ASN cc_start: 0.8531 (m110) cc_final: 0.8011 (m-40) REVERT: F 91 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8707 (ttpp) REVERT: H 113 GLU cc_start: 0.8517 (tp30) cc_final: 0.7537 (tm-30) REVERT: K 20 MET cc_start: 0.7069 (mmp) cc_final: 0.6740 (mpp) REVERT: K 64 TYR cc_start: 0.8618 (t80) cc_final: 0.8261 (t80) REVERT: C 92 GLU cc_start: 0.8092 (mp0) cc_final: 0.7792 (mp0) REVERT: C 104 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8623 (tp40) REVERT: G 36 LYS cc_start: 0.8265 (pttt) cc_final: 0.7858 (mmtp) outliers start: 12 outliers final: 6 residues processed: 164 average time/residue: 0.3682 time to fit residues: 79.7084 Evaluate side-chains 144 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 0.0770 chunk 99 optimal weight: 0.0270 chunk 110 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.166 Angle : 0.539 6.285 21358 Z= 0.315 Chirality : 0.034 0.139 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.279 158.072 4324 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.81 % Allowed : 13.60 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.08 (0.27), residues: 989 helix: 1.76 (0.21), residues: 657 sheet: -0.35 (1.19), residues: 23 loop : -1.55 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.011 0.001 PHE L 69 TYR 0.023 0.001 TYR H 121 ARG 0.005 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9174 (m-80) cc_final: 0.8830 (m-80) REVERT: A 59 GLU cc_start: 0.8092 (pm20) cc_final: 0.7789 (pm20) REVERT: A 134 ARG cc_start: 0.5935 (OUTLIER) cc_final: 0.5510 (ptt-90) REVERT: B 84 MET cc_start: 0.8404 (mmm) cc_final: 0.8113 (mmm) REVERT: D 68 ASP cc_start: 0.8900 (t70) cc_final: 0.8633 (t0) REVERT: D 83 TYR cc_start: 0.8539 (m-10) cc_final: 0.8022 (m-80) REVERT: D 108 LYS cc_start: 0.7713 (ttpt) cc_final: 0.7448 (mtpp) REVERT: D 120 LYS cc_start: 0.8914 (tttp) cc_final: 0.8693 (tttp) REVERT: F 25 ASN cc_start: 0.8562 (m110) cc_final: 0.8063 (m-40) REVERT: F 91 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8610 (ttpp) REVERT: H 113 GLU cc_start: 0.8450 (tp30) cc_final: 0.8055 (tm-30) REVERT: K 20 MET cc_start: 0.7153 (mmp) cc_final: 0.6840 (mpp) REVERT: C 92 GLU cc_start: 0.8041 (mp0) cc_final: 0.7741 (mp0) REVERT: C 104 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8610 (tp40) REVERT: G 36 LYS cc_start: 0.8232 (pttt) cc_final: 0.7799 (mmtp) outliers start: 7 outliers final: 4 residues processed: 171 average time/residue: 0.3266 time to fit residues: 76.2642 Evaluate side-chains 149 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain G residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 0.0370 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.0370 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.193 Angle : 0.551 8.951 21358 Z= 0.318 Chirality : 0.034 0.139 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.327 157.926 4324 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.09 % Allowed : 14.88 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.42 (0.27), residues: 989 helix: 1.99 (0.20), residues: 657 sheet: -0.19 (1.22), residues: 23 loop : -1.33 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 61 HIS 0.005 0.001 HIS K 65 PHE 0.012 0.001 PHE K 53 TYR 0.025 0.001 TYR H 121 ARG 0.005 0.000 ARG K 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9206 (m-80) cc_final: 0.8866 (m-80) REVERT: A 59 GLU cc_start: 0.8043 (pm20) cc_final: 0.7699 (pm20) REVERT: A 134 ARG cc_start: 0.6058 (OUTLIER) cc_final: 0.5662 (ptt-90) REVERT: B 84 MET cc_start: 0.8424 (mmm) cc_final: 0.8139 (mmm) REVERT: D 68 ASP cc_start: 0.8904 (t70) cc_final: 0.8626 (t0) REVERT: D 83 TYR cc_start: 0.8636 (m-10) cc_final: 0.8275 (m-80) REVERT: D 101 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 108 LYS cc_start: 0.7752 (ttpt) cc_final: 0.7409 (mtpp) REVERT: F 25 ASN cc_start: 0.8554 (m110) cc_final: 0.8036 (m-40) REVERT: F 91 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8621 (ttpp) REVERT: K 20 MET cc_start: 0.7111 (mmp) cc_final: 0.6854 (mpp) REVERT: C 92 GLU cc_start: 0.8068 (mp0) cc_final: 0.7815 (mp0) REVERT: C 104 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8581 (tp40) REVERT: G 36 LYS cc_start: 0.8276 (pttt) cc_final: 0.7899 (mmtp) REVERT: G 72 ASP cc_start: 0.8931 (m-30) cc_final: 0.8527 (m-30) outliers start: 18 outliers final: 9 residues processed: 151 average time/residue: 0.3696 time to fit residues: 74.3846 Evaluate side-chains 150 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN H 84 ASN K 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.185 Angle : 0.536 8.052 21358 Z= 0.313 Chirality : 0.034 0.138 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.216 158.011 4324 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.63 % Allowed : 15.93 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.69 (0.27), residues: 989 helix: 2.15 (0.21), residues: 658 sheet: 0.15 (1.20), residues: 23 loop : -1.12 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.016 0.001 PHE K 53 TYR 0.025 0.001 TYR H 121 ARG 0.005 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7942 (pm20) cc_final: 0.7720 (pm20) REVERT: A 134 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5607 (ptt-90) REVERT: B 84 MET cc_start: 0.8401 (mmm) cc_final: 0.8110 (mmm) REVERT: D 68 ASP cc_start: 0.8892 (t70) cc_final: 0.8612 (t0) REVERT: D 83 TYR cc_start: 0.8639 (m-10) cc_final: 0.8251 (m-80) REVERT: D 108 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7461 (ttmm) REVERT: F 25 ASN cc_start: 0.8537 (m110) cc_final: 0.8046 (m-40) REVERT: F 91 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8608 (ttpp) REVERT: C 92 GLU cc_start: 0.8079 (mp0) cc_final: 0.7842 (mp0) REVERT: C 104 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8424 (tp40) REVERT: G 36 LYS cc_start: 0.8315 (pttt) cc_final: 0.7893 (mmtp) REVERT: G 72 ASP cc_start: 0.8931 (m-30) cc_final: 0.8545 (m-30) outliers start: 14 outliers final: 11 residues processed: 142 average time/residue: 0.3506 time to fit residues: 66.9437 Evaluate side-chains 145 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ARG Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN L 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14874 Z= 0.256 Angle : 0.563 8.480 21358 Z= 0.325 Chirality : 0.035 0.140 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.540 157.347 4324 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.21 % Allowed : 16.28 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.64 (0.27), residues: 989 helix: 2.07 (0.21), residues: 660 sheet: 0.56 (1.23), residues: 23 loop : -1.10 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.015 0.001 PHE K 53 TYR 0.028 0.002 TYR H 121 ARG 0.004 0.000 ARG H 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9173 (m-80) cc_final: 0.8831 (m-80) REVERT: A 59 GLU cc_start: 0.7946 (pm20) cc_final: 0.7701 (pm20) REVERT: B 84 MET cc_start: 0.8538 (mmm) cc_final: 0.8164 (mmm) REVERT: D 68 ASP cc_start: 0.8908 (t70) cc_final: 0.8598 (t0) REVERT: D 87 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8583 (p) REVERT: D 101 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8641 (mp) REVERT: D 108 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7411 (mtpp) REVERT: F 25 ASN cc_start: 0.8538 (m110) cc_final: 0.8066 (m-40) REVERT: C 92 GLU cc_start: 0.8131 (mp0) cc_final: 0.7927 (mp0) REVERT: C 104 GLN cc_start: 0.8804 (mm-40) cc_final: 0.8411 (tp40) REVERT: G 36 LYS cc_start: 0.8325 (pttt) cc_final: 0.7906 (mmtp) outliers start: 19 outliers final: 12 residues processed: 141 average time/residue: 0.3524 time to fit residues: 66.3112 Evaluate side-chains 143 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 14874 Z= 0.451 Angle : 0.652 8.721 21358 Z= 0.371 Chirality : 0.041 0.172 2420 Planarity : 0.005 0.057 1691 Dihedral : 30.150 157.270 4324 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.44 % Allowed : 16.98 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.24 (0.27), residues: 989 helix: 1.74 (0.20), residues: 656 sheet: 0.78 (1.24), residues: 23 loop : -1.20 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 61 HIS 0.003 0.001 HIS E 113 PHE 0.015 0.002 PHE K 53 TYR 0.031 0.002 TYR H 121 ARG 0.010 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8632 (mmm) cc_final: 0.8134 (mmm) REVERT: D 68 ASP cc_start: 0.8952 (t70) cc_final: 0.8643 (t0) REVERT: D 83 TYR cc_start: 0.8872 (m-10) cc_final: 0.8559 (m-80) REVERT: D 87 SER cc_start: 0.9026 (OUTLIER) cc_final: 0.8648 (p) REVERT: D 101 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8636 (mp) REVERT: D 108 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7436 (mtpp) REVERT: F 25 ASN cc_start: 0.8594 (m110) cc_final: 0.8088 (m-40) REVERT: H 113 GLU cc_start: 0.8554 (tp30) cc_final: 0.7619 (tm-30) REVERT: L 65 PRO cc_start: 0.6706 (Cg_endo) cc_final: 0.6284 (Cg_exo) REVERT: C 92 GLU cc_start: 0.8243 (mp0) cc_final: 0.8010 (mp0) REVERT: C 104 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8428 (tp40) REVERT: G 36 LYS cc_start: 0.8353 (pttt) cc_final: 0.7933 (mmtp) outliers start: 21 outliers final: 14 residues processed: 148 average time/residue: 0.3431 time to fit residues: 67.9862 Evaluate side-chains 149 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 42 ASP Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 0.1980 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 40.0000 chunk 107 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.179 Angle : 0.550 8.802 21358 Z= 0.321 Chirality : 0.034 0.182 2420 Planarity : 0.004 0.040 1691 Dihedral : 29.271 159.935 4324 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.40 % Allowed : 18.26 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.67 (0.27), residues: 989 helix: 2.09 (0.20), residues: 658 sheet: 0.83 (1.23), residues: 23 loop : -1.10 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 61 HIS 0.004 0.001 HIS A 113 PHE 0.018 0.001 PHE K 53 TYR 0.024 0.001 TYR H 121 ARG 0.007 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9088 (m-80) cc_final: 0.8720 (m-80) REVERT: A 90 MET cc_start: 0.8033 (mmm) cc_final: 0.7740 (mmp) REVERT: B 84 MET cc_start: 0.8368 (mmm) cc_final: 0.8089 (mmm) REVERT: D 62 MET cc_start: 0.9113 (mmm) cc_final: 0.8897 (mmm) REVERT: D 68 ASP cc_start: 0.8856 (t70) cc_final: 0.8577 (t0) REVERT: F 25 ASN cc_start: 0.8562 (m110) cc_final: 0.8097 (m-40) REVERT: H 37 TYR cc_start: 0.9011 (m-80) cc_final: 0.8767 (m-80) REVERT: L 65 PRO cc_start: 0.6539 (Cg_endo) cc_final: 0.6110 (Cg_exo) REVERT: C 92 GLU cc_start: 0.8079 (mp0) cc_final: 0.7836 (mp0) REVERT: C 104 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8455 (tp40) REVERT: G 36 LYS cc_start: 0.8272 (pttt) cc_final: 0.7842 (mmtp) REVERT: G 104 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8188 (mm-40) outliers start: 12 outliers final: 10 residues processed: 146 average time/residue: 0.3486 time to fit residues: 68.2973 Evaluate side-chains 144 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14874 Z= 0.174 Angle : 0.544 9.083 21358 Z= 0.316 Chirality : 0.034 0.141 2420 Planarity : 0.004 0.040 1691 Dihedral : 29.284 159.952 4324 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.16 % Allowed : 18.26 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.27), residues: 989 helix: 2.23 (0.20), residues: 659 sheet: 0.83 (1.22), residues: 23 loop : -0.94 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 61 HIS 0.003 0.000 HIS A 113 PHE 0.018 0.001 PHE K 53 TYR 0.025 0.002 TYR H 121 ARG 0.007 0.000 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9098 (m-80) cc_final: 0.8725 (m-80) REVERT: A 90 MET cc_start: 0.8086 (mmm) cc_final: 0.7785 (mmt) REVERT: D 68 ASP cc_start: 0.8867 (t70) cc_final: 0.8596 (t0) REVERT: D 101 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8620 (mp) REVERT: F 25 ASN cc_start: 0.8534 (m110) cc_final: 0.8041 (m-40) REVERT: F 88 TYR cc_start: 0.8562 (m-80) cc_final: 0.8296 (m-80) REVERT: H 37 TYR cc_start: 0.9027 (m-80) cc_final: 0.8801 (m-80) REVERT: L 65 PRO cc_start: 0.6528 (Cg_endo) cc_final: 0.6093 (Cg_exo) REVERT: C 92 GLU cc_start: 0.8088 (mp0) cc_final: 0.7859 (mp0) REVERT: C 104 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8438 (tp40) REVERT: G 36 LYS cc_start: 0.8287 (pttt) cc_final: 0.7837 (mmtp) REVERT: G 72 ASP cc_start: 0.8917 (m-30) cc_final: 0.8556 (m-30) REVERT: G 92 GLU cc_start: 0.8429 (mp0) cc_final: 0.8046 (mp0) outliers start: 10 outliers final: 8 residues processed: 136 average time/residue: 0.3577 time to fit residues: 65.7871 Evaluate side-chains 143 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 122 optimal weight: 0.0570 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14874 Z= 0.399 Angle : 0.640 9.594 21358 Z= 0.361 Chirality : 0.039 0.160 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.789 157.305 4324 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.16 % Allowed : 18.37 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.43 (0.27), residues: 989 helix: 1.88 (0.20), residues: 657 sheet: 0.86 (1.22), residues: 23 loop : -1.11 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 61 HIS 0.004 0.001 HIS D 49 PHE 0.019 0.002 PHE K 53 TYR 0.034 0.003 TYR H 121 ARG 0.005 0.000 ARG D 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1978 Ramachandran restraints generated. 989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9195 (m-80) cc_final: 0.8865 (m-80) REVERT: B 88 TYR cc_start: 0.8637 (m-10) cc_final: 0.8285 (m-80) REVERT: D 68 ASP cc_start: 0.8922 (t70) cc_final: 0.8636 (t0) REVERT: D 101 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8618 (mp) REVERT: D 108 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7404 (mtpp) REVERT: F 25 ASN cc_start: 0.8558 (m110) cc_final: 0.8061 (m-40) REVERT: F 88 TYR cc_start: 0.8617 (m-80) cc_final: 0.8271 (m-80) REVERT: L 65 PRO cc_start: 0.6564 (Cg_endo) cc_final: 0.6140 (Cg_exo) REVERT: C 92 GLU cc_start: 0.8247 (mp0) cc_final: 0.8033 (mp0) REVERT: G 36 LYS cc_start: 0.8271 (pttt) cc_final: 0.7940 (mmtp) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 0.3376 time to fit residues: 61.8395 Evaluate side-chains 140 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 112 ASP Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 27 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.142989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085871 restraints weight = 36000.851| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.97 r_work: 0.2889 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14874 Z= 0.178 Angle : 0.555 9.298 21358 Z= 0.320 Chirality : 0.034 0.152 2420 Planarity : 0.004 0.040 1691 Dihedral : 29.302 159.939 4324 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.16 % Allowed : 18.49 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.82 (0.27), residues: 989 helix: 2.17 (0.20), residues: 657 sheet: 0.92 (1.21), residues: 23 loop : -0.94 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 61 HIS 0.003 0.000 HIS A 113 PHE 0.021 0.001 PHE K 53 TYR 0.026 0.002 TYR H 121 ARG 0.006 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.64 seconds wall clock time: 52 minutes 4.21 seconds (3124.21 seconds total)