Starting phenix.real_space_refine on Wed Aug 7 02:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/08_2024/8upf_42446.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/08_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_42446/08_2024/8upf_42446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/08_2024/8upf_42446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/08_2024/8upf_42446.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8upf_42446/08_2024/8upf_42446.cif" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 8.55, per 1000 atoms: 0.61 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: 7.91 Conformation dependent library (CDL) restraints added in 1.7 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: 6.68 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: 5.53 Time building geometry restraints manager: 8.12 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 3.040 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.163 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 49.470 Find NCS groups from input model: 0.580 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.120 ------------------------------------------------------------------------------- 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 : 1.129 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: 0.4419 time to fit residues: 100.3117 Evaluate side-chains 156 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14874 Z= 0.295 Angle : 0.603 5.840 21358 Z= 0.348 Chirality : 0.037 0.162 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.905 156.174 4324 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 10.58 % Favored : 88.37 % 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: -0.19 (0.26), residues: 989 helix: 0.78 (0.20), residues: 656 sheet: -1.20 (1.05), residues: 23 loop : -1.97 (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 0.012 0.002 PHE L 62 TYR 0.024 0.002 TYR H 121 ARG 0.005 0.000 ARG E 134 *********************** 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 165 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8348 (pm20) cc_final: 0.8093 (pm20) REVERT: D 47 GLN cc_start: 0.8675 (mt0) cc_final: 0.8397 (tt0) REVERT: D 68 ASP cc_start: 0.9008 (t70) cc_final: 0.8754 (t0) REVERT: D 108 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7401 (mtpp) REVERT: F 25 ASN cc_start: 0.8521 (m110) cc_final: 0.7991 (m-40) REVERT: F 91 LYS cc_start: 0.9014 (ttmt) cc_final: 0.8678 (ttpp) REVERT: H 113 GLU cc_start: 0.8549 (tp30) cc_final: 0.7575 (tm-30) REVERT: K 20 MET cc_start: 0.7219 (mmp) cc_final: 0.6873 (mpp) REVERT: C 24 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8441 (mm-40) REVERT: C 61 GLU cc_start: 0.8260 (tp30) cc_final: 0.8050 (tt0) REVERT: C 92 GLU cc_start: 0.8123 (mp0) cc_final: 0.7852 (mp0) REVERT: C 104 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8647 (tp40) REVERT: G 36 LYS cc_start: 0.8324 (pttt) cc_final: 0.7863 (mmtp) REVERT: G 92 GLU cc_start: 0.8441 (mp0) cc_final: 0.7502 (mp0) outliers start: 9 outliers final: 4 residues processed: 160 average time/residue: 0.3727 time to fit residues: 78.3693 Evaluate side-chains 141 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain L residue 99 ILE 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: 0.7980 chunk 92 optimal weight: 0.0370 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 99 optimal weight: 30.0000 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 27 GLN F 93 GLN H 84 ASN G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14874 Z= 0.170 Angle : 0.548 6.643 21358 Z= 0.320 Chirality : 0.034 0.134 2420 Planarity : 0.004 0.036 1691 Dihedral : 29.241 158.539 4324 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.40 % Allowed : 13.95 % Favored : 84.65 % 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: 1.06 (0.27), residues: 989 helix: 1.78 (0.20), residues: 657 sheet: -0.30 (1.18), residues: 23 loop : -1.64 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 77 HIS 0.005 0.001 HIS K 65 PHE 0.007 0.001 PHE L 69 TYR 0.024 0.001 TYR H 121 ARG 0.004 0.000 ARG E 134 *********************** 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 180 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8120 (pm20) cc_final: 0.7780 (pm20) REVERT: A 90 MET cc_start: 0.8005 (mmp) cc_final: 0.7796 (mmt) REVERT: A 134 ARG cc_start: 0.5740 (OUTLIER) cc_final: 0.5438 (ptt-90) REVERT: D 83 TYR cc_start: 0.8587 (m-10) cc_final: 0.8212 (m-80) REVERT: D 108 LYS cc_start: 0.7689 (ttpt) cc_final: 0.7463 (ttmm) REVERT: F 25 ASN cc_start: 0.8549 (m110) cc_final: 0.8046 (m-40) REVERT: F 77 LYS cc_start: 0.9131 (mttt) cc_final: 0.8870 (mtmt) REVERT: F 91 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8638 (ttpp) REVERT: H 113 GLU cc_start: 0.8435 (tp30) cc_final: 0.8050 (tm-30) REVERT: K 20 MET cc_start: 0.7350 (mmp) cc_final: 0.6875 (mpp) REVERT: C 92 GLU cc_start: 0.8134 (mp0) cc_final: 0.7797 (mp0) REVERT: C 104 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8625 (tp40) REVERT: G 36 LYS cc_start: 0.8236 (pttt) cc_final: 0.7836 (mmtp) REVERT: G 72 ASP cc_start: 0.8948 (m-30) cc_final: 0.8515 (m-30) REVERT: G 92 GLU cc_start: 0.8513 (mp0) cc_final: 0.7396 (mp0) REVERT: G 104 GLN cc_start: 0.8454 (mm110) cc_final: 0.8195 (mm-40) outliers start: 12 outliers final: 6 residues processed: 173 average time/residue: 0.3458 time to fit residues: 81.4125 Evaluate side-chains 150 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 58 THR 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: 2.9990 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 14874 Z= 0.446 Angle : 0.659 8.470 21358 Z= 0.371 Chirality : 0.040 0.159 2420 Planarity : 0.005 0.038 1691 Dihedral : 30.074 157.298 4324 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.98 % Allowed : 16.16 % Favored : 81.86 % 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: 0.83 (0.27), residues: 989 helix: 1.60 (0.20), residues: 656 sheet: -0.30 (1.20), residues: 23 loop : -1.72 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.016 0.002 PHE E 78 TYR 0.031 0.002 TYR H 121 ARG 0.004 0.000 ARG H 99 *********************** 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 151 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8685 (m-10) cc_final: 0.8388 (m-80) REVERT: D 108 LYS cc_start: 0.7835 (ttpt) cc_final: 0.7398 (mtpp) REVERT: F 25 ASN cc_start: 0.8577 (m110) cc_final: 0.8087 (m-40) REVERT: F 88 TYR cc_start: 0.8714 (m-80) cc_final: 0.8436 (m-80) REVERT: F 91 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8676 (ttpp) REVERT: H 113 GLU cc_start: 0.8546 (tp30) cc_final: 0.7542 (tm-30) REVERT: C 61 GLU cc_start: 0.8299 (tp30) cc_final: 0.8036 (tt0) REVERT: C 104 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8612 (tp40) REVERT: G 36 LYS cc_start: 0.8360 (pttt) cc_final: 0.7965 (mmtp) REVERT: G 92 GLU cc_start: 0.8496 (mp0) cc_final: 0.7645 (mp0) outliers start: 17 outliers final: 8 residues processed: 145 average time/residue: 0.3585 time to fit residues: 69.5757 Evaluate side-chains 135 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 118 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 101 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2643 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= 0.190 Angle : 0.554 7.409 21358 Z= 0.322 Chirality : 0.034 0.163 2420 Planarity : 0.004 0.037 1691 Dihedral : 29.381 159.395 4324 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.86 % Allowed : 16.05 % Favored : 82.09 % 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: 1.33 (0.27), residues: 989 helix: 1.95 (0.20), residues: 659 sheet: -0.02 (1.10), residues: 23 loop : -1.48 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.015 0.001 PHE K 53 TYR 0.024 0.001 TYR H 121 ARG 0.004 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 158 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8585 (mmm) cc_final: 0.8156 (mmm) REVERT: D 83 TYR cc_start: 0.8673 (m-10) cc_final: 0.8113 (m-80) REVERT: D 108 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7454 (ttmm) REVERT: F 25 ASN cc_start: 0.8545 (m110) cc_final: 0.8076 (m-40) REVERT: F 88 TYR cc_start: 0.8561 (m-80) cc_final: 0.8220 (m-80) REVERT: F 91 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8618 (ttpp) REVERT: K 20 MET cc_start: 0.7346 (mmm) cc_final: 0.6901 (mpp) REVERT: C 104 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8600 (tp40) REVERT: G 36 LYS cc_start: 0.8239 (pttt) cc_final: 0.7905 (mmtp) REVERT: G 84 GLN cc_start: 0.8942 (tp-100) cc_final: 0.8687 (tp-100) REVERT: G 92 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (mt-10) outliers start: 16 outliers final: 10 residues processed: 148 average time/residue: 0.3304 time to fit residues: 66.2806 Evaluate side-chains 148 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 114 optimal weight: 0.0770 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2734 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= 0.207 Angle : 0.552 7.325 21358 Z= 0.321 Chirality : 0.035 0.142 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.421 159.391 4324 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.74 % Allowed : 17.21 % Favored : 81.05 % 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: 1.50 (0.27), residues: 989 helix: 2.02 (0.20), residues: 659 sheet: 0.46 (1.14), residues: 23 loop : -1.32 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.018 0.001 PHE K 53 TYR 0.027 0.001 TYR H 121 ARG 0.007 0.000 ARG D 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 149 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 108 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7471 (ttmm) REVERT: F 25 ASN cc_start: 0.8509 (m110) cc_final: 0.8031 (m-40) REVERT: F 88 TYR cc_start: 0.8554 (m-80) cc_final: 0.8032 (m-80) REVERT: F 91 LYS cc_start: 0.8996 (ttmt) cc_final: 0.8623 (ttpp) REVERT: H 37 TYR cc_start: 0.9023 (m-80) cc_final: 0.8783 (m-80) REVERT: K 20 MET cc_start: 0.7366 (mmm) cc_final: 0.6935 (mpp) REVERT: C 104 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8598 (tp40) REVERT: G 36 LYS cc_start: 0.8268 (pttt) cc_final: 0.7908 (mmtp) REVERT: G 92 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8132 (mt-10) outliers start: 15 outliers final: 10 residues processed: 141 average time/residue: 0.3545 time to fit residues: 67.8989 Evaluate side-chains 151 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 15 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 14874 Z= 0.475 Angle : 0.669 10.881 21358 Z= 0.378 Chirality : 0.041 0.174 2420 Planarity : 0.005 0.036 1691 Dihedral : 30.141 157.774 4324 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.74 % Allowed : 17.33 % Favored : 80.93 % 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: 1.02 (0.27), residues: 989 helix: 1.64 (0.20), residues: 656 sheet: 0.55 (1.21), residues: 23 loop : -1.45 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP K 61 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.002 PHE K 53 TYR 0.033 0.002 TYR H 121 ARG 0.004 0.000 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 161 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8083 (pm20) cc_final: 0.7754 (pm20) REVERT: B 84 MET cc_start: 0.8674 (mmm) cc_final: 0.8167 (mmm) REVERT: B 88 TYR cc_start: 0.8585 (m-10) cc_final: 0.7999 (m-80) REVERT: D 101 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 108 LYS cc_start: 0.7873 (ttpt) cc_final: 0.7425 (mtpp) REVERT: F 25 ASN cc_start: 0.8564 (m110) cc_final: 0.8103 (m-40) REVERT: L 65 PRO cc_start: 0.6763 (Cg_endo) cc_final: 0.6382 (Cg_exo) REVERT: C 104 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8557 (tp40) REVERT: G 36 LYS cc_start: 0.8370 (pttt) cc_final: 0.7948 (mmtp) REVERT: G 92 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8239 (mt-10) outliers start: 15 outliers final: 9 residues processed: 153 average time/residue: 0.3511 time to fit residues: 71.8667 Evaluate side-chains 146 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 92 GLU 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: 2.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 11 optimal weight: 0.3980 chunk 93 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2927 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= 0.186 Angle : 0.564 10.324 21358 Z= 0.328 Chirality : 0.035 0.139 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.339 160.056 4324 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.86 % Allowed : 17.91 % Favored : 80.23 % 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: 1.46 (0.27), residues: 989 helix: 1.98 (0.20), residues: 659 sheet: 0.77 (1.21), residues: 23 loop : -1.34 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.006 0.001 HIS K 65 PHE 0.018 0.001 PHE K 53 TYR 0.033 0.002 TYR F 88 ARG 0.006 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 157 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8425 (mmm) cc_final: 0.8091 (mmm) REVERT: D 62 MET cc_start: 0.9059 (mmm) cc_final: 0.8845 (mmm) REVERT: F 25 ASN cc_start: 0.8544 (m110) cc_final: 0.8091 (m-40) REVERT: F 91 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8470 (ttpp) REVERT: K 20 MET cc_start: 0.7299 (mmm) cc_final: 0.6913 (mpp) REVERT: L 65 PRO cc_start: 0.6729 (Cg_endo) cc_final: 0.6347 (Cg_exo) REVERT: C 104 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8479 (tp40) REVERT: G 36 LYS cc_start: 0.8247 (pttt) cc_final: 0.7902 (mmtp) REVERT: G 92 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8194 (mt-10) REVERT: G 104 GLN cc_start: 0.8475 (mm-40) cc_final: 0.8271 (mm-40) outliers start: 16 outliers final: 12 residues processed: 148 average time/residue: 0.3278 time to fit residues: 66.1181 Evaluate side-chains 148 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.168 ------------------------------------------------------------------------------- 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 D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.2980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3037 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= 0.178 Angle : 0.558 10.129 21358 Z= 0.324 Chirality : 0.034 0.139 2420 Planarity : 0.004 0.039 1691 Dihedral : 29.296 160.329 4324 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 18.95 % Favored : 80.00 % 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: 1.68 (0.27), residues: 989 helix: 2.14 (0.20), residues: 658 sheet: 0.81 (1.20), residues: 23 loop : -1.22 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.019 0.001 PHE K 53 TYR 0.027 0.002 TYR F 88 ARG 0.005 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 145 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8387 (mmm) cc_final: 0.8045 (mmm) REVERT: F 25 ASN cc_start: 0.8529 (m110) cc_final: 0.8089 (m-40) REVERT: H 37 TYR cc_start: 0.9010 (m-80) cc_final: 0.8768 (m-80) REVERT: K 20 MET cc_start: 0.7295 (mmm) cc_final: 0.6910 (mpp) REVERT: L 65 PRO cc_start: 0.6673 (Cg_endo) cc_final: 0.6279 (Cg_exo) REVERT: G 36 LYS cc_start: 0.8221 (pttt) cc_final: 0.7893 (mmtp) REVERT: G 72 ASP cc_start: 0.8920 (m-30) cc_final: 0.8564 (m-30) REVERT: G 89 ASN cc_start: 0.8954 (m-40) cc_final: 0.8737 (m-40) REVERT: G 92 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8190 (mt-10) outliers start: 9 outliers final: 7 residues processed: 138 average time/residue: 0.3512 time to fit residues: 65.4821 Evaluate side-chains 141 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 133 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 92 GLU 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: 0.2980 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 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: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.8061 moved from start: 0.3013 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= 0.248 Angle : 0.580 9.930 21358 Z= 0.333 Chirality : 0.035 0.140 2420 Planarity : 0.004 0.038 1691 Dihedral : 29.424 159.417 4324 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 19.07 % Favored : 79.88 % 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: 1.62 (0.27), residues: 989 helix: 2.08 (0.20), residues: 661 sheet: 0.86 (1.21), residues: 23 loop : -1.23 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.004 0.001 HIS D 49 PHE 0.020 0.001 PHE K 53 TYR 0.027 0.002 TYR H 121 ARG 0.004 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 148 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7899 (pm20) cc_final: 0.7596 (pm20) REVERT: B 84 MET cc_start: 0.8484 (mmm) cc_final: 0.8123 (mmm) REVERT: D 62 MET cc_start: 0.9086 (mmm) cc_final: 0.8852 (mmm) REVERT: D 83 TYR cc_start: 0.8825 (m-10) cc_final: 0.8549 (m-80) REVERT: D 101 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8620 (mp) REVERT: D 108 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7482 (ttmm) REVERT: F 25 ASN cc_start: 0.8528 (m110) cc_final: 0.8077 (m-40) REVERT: H 37 TYR cc_start: 0.9024 (m-80) cc_final: 0.8769 (m-80) REVERT: K 20 MET cc_start: 0.7239 (mmm) cc_final: 0.6877 (mpp) REVERT: L 65 PRO cc_start: 0.6669 (Cg_endo) cc_final: 0.6273 (Cg_exo) REVERT: G 36 LYS cc_start: 0.8251 (pttt) cc_final: 0.7878 (mmtp) REVERT: G 92 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8260 (mt-10) outliers start: 9 outliers final: 7 residues processed: 144 average time/residue: 0.3667 time to fit residues: 70.9525 Evaluate side-chains 147 residues out of total 854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 100 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.143897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.087232 restraints weight = 35946.649| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.94 r_work: 0.2918 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2927 r_free = 0.2927 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3256 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= 0.173 Angle : 0.557 9.661 21358 Z= 0.322 Chirality : 0.034 0.137 2420 Planarity : 0.004 0.051 1691 Dihedral : 29.096 160.097 4324 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 18.84 % Favored : 79.88 % 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: 2.23 (0.20), residues: 659 sheet: 1.08 (1.22), residues: 23 loop : -1.13 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.020 0.001 PHE K 53 TYR 0.024 0.002 TYR H 121 ARG 0.009 0.000 ARG D 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.15 seconds wall clock time: 54 minutes 6.05 seconds (3246.05 seconds total)