Starting phenix.real_space_refine on Sun Nov 17 17:12:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/11_2024/8sn3_40611.cif" } resolution = 3.8 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8276 2.51 5 N 2716 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14612 Number of models: 1 Model: "" Number of chains: 14 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: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} 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: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} 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: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 704 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} 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 12313 SG CYS K 31 31.696 74.358 48.206 1.00 55.65 S ATOM 12463 SG CYS K 51 30.684 71.325 47.252 1.00 54.45 S ATOM 12487 SG CYS K 54 31.262 73.831 44.365 1.00 65.71 S ATOM 12204 SG CYS K 16 21.823 68.573 53.938 1.00 64.66 S ATOM 12222 SG CYS K 19 19.688 65.906 55.446 1.00 64.84 S ATOM 12352 SG CYS K 36 22.524 67.475 57.565 1.00 50.00 S ATOM 12374 SG CYS K 39 23.418 65.177 54.865 1.00 54.15 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 76 " occ=0.25 Time building chain proxies: 8.68, per 1000 atoms: 0.59 Number of scatterers: 14612 At special positions: 0 Unit cell: (108.896, 134.128, 126.16, 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 33 16.00 P 294 15.00 O 3291 8.00 N 2716 7.00 C 8276 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 - 3.00 Amino acid : True - 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: 4.05 Conformation dependent library (CDL) restraints added in 1.4 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=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 6 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 63.1% alpha, 4.5% beta 135 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.659A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.773A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (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 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.748A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.523A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.713A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.714A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.649A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.002A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.534A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.673A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.837A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.774A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 4.669A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 90 removed outlier: 3.792A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.710A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.549A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.564A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.900A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.863A pdb=" N TYR M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A 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 'C' and resid 42 through 43 removed outlier: 8.120A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.878A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24 removed outlier: 4.097A pdb=" N SER L 22 " --> pdb=" O THR L 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 removed outlier: 3.627A pdb=" N ILE M 13 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3244 1.33 - 1.45: 4467 1.45 - 1.57: 7137 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15483 Sorted by residual: bond pdb=" CD LYS D 116 " pdb=" CE LYS D 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG LYS D 116 " pdb=" CD LYS D 116 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 15478 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 21491 1.43 - 2.85: 626 2.85 - 4.28: 39 4.28 - 5.70: 22 5.70 - 7.13: 4 Bond angle restraints: 22182 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 111.90 108.81 3.09 8.10e-01 1.52e+00 1.45e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" CA LYS D 116 " pdb=" CB LYS D 116 " pdb=" CG LYS D 116 " ideal model delta sigma weight residual 114.10 108.74 5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" C ALA K 47 " pdb=" N SER K 48 " pdb=" CA SER K 48 " ideal model delta sigma weight residual 122.55 117.60 4.95 2.03e+00 2.43e-01 5.94e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.57 7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 22177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7299 35.74 - 71.48: 1293 71.48 - 107.22: 17 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: 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 -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA GLN M 41 " pdb=" C GLN M 41 " pdb=" N ARG M 42 " pdb=" CA ARG M 42 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+01 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 74.33 145.67 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1731 0.029 - 0.059: 577 0.059 - 0.088: 134 0.088 - 0.117: 66 0.117 - 0.146: 8 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2513 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.019 2.00e-02 2.50e+03 1.74e-02 6.06e+00 pdb=" CG TYR F 88 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 37 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO M 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO M 38 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 38 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.010 2.00e-02 2.50e+03 1.33e-02 3.53e+00 pdb=" CG TYR B 88 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1938 2.76 - 3.47: 19786 3.47 - 4.19: 38128 4.19 - 4.90: 59060 Nonbonded interactions: 118914 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.164 2.496 nonbonded pdb=" O ARG L 139 " pdb=" NE2 GLN L 143 " model vdw 2.205 3.120 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.251 3.120 ... (remaining 118909 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 118) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.720 Find NCS groups from input model: 0.340 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 : 0.003 0.040 15483 Z= 0.201 Angle : 0.553 7.129 22182 Z= 0.322 Chirality : 0.034 0.146 2516 Planarity : 0.004 0.075 1795 Dihedral : 25.549 178.698 6581 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1058 helix: 2.28 (0.21), residues: 634 sheet: 1.13 (0.76), residues: 46 loop : -0.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE K 53 TYR 0.043 0.002 TYR F 88 ARG 0.004 0.000 ARG M 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm) REVERT: D 68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0) REVERT: G 36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8418 (mmtm) REVERT: H 120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt) REVERT: K 41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40) REVERT: K 68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3662 time to fit residues: 109.7013 Evaluate side-chains 182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 GLN L 79 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15483 Z= 0.207 Angle : 0.578 10.630 22182 Z= 0.331 Chirality : 0.034 0.175 2516 Planarity : 0.004 0.036 1795 Dihedral : 28.773 178.855 4412 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.84 % Allowed : 11.14 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.00 (0.26), residues: 1058 helix: 2.33 (0.21), residues: 651 sheet: 1.24 (0.87), residues: 38 loop : -0.53 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 141 HIS 0.004 0.001 HIS L 75 PHE 0.010 0.001 PHE A 67 TYR 0.034 0.002 TYR H 83 ARG 0.009 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9023 (mttm) cc_final: 0.8567 (mttm) REVERT: C 95 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8700 (tttm) REVERT: D 40 TYR cc_start: 0.9366 (m-80) cc_final: 0.9153 (m-80) REVERT: D 59 MET cc_start: 0.8827 (tpp) cc_final: 0.8591 (tpp) REVERT: D 68 ASP cc_start: 0.8287 (t70) cc_final: 0.8054 (t0) REVERT: D 83 TYR cc_start: 0.7799 (m-10) cc_final: 0.7192 (m-80) REVERT: G 36 LYS cc_start: 0.8803 (mptt) cc_final: 0.8529 (mmtm) REVERT: H 42 TYR cc_start: 0.8550 (t80) cc_final: 0.8176 (t80) REVERT: H 120 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8950 (ttpt) REVERT: L 5 ARG cc_start: 0.7760 (tpt90) cc_final: 0.7303 (tpt90) REVERT: L 9 GLU cc_start: 0.6641 (tt0) cc_final: 0.6177 (tt0) REVERT: L 101 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8081 (mmmm) REVERT: L 147 MET cc_start: 0.4043 (mpp) cc_final: 0.3641 (mpp) REVERT: M 1 MET cc_start: -0.0722 (OUTLIER) cc_final: -0.0924 (ptt) outliers start: 17 outliers final: 12 residues processed: 201 average time/residue: 0.3474 time to fit residues: 95.0781 Evaluate side-chains 194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain M residue 1 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15483 Z= 0.382 Angle : 0.636 11.154 22182 Z= 0.359 Chirality : 0.038 0.174 2516 Planarity : 0.005 0.043 1795 Dihedral : 29.061 178.493 4412 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.49 % Allowed : 13.95 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 (0.26), residues: 1058 helix: 2.05 (0.20), residues: 654 sheet: 0.98 (0.83), residues: 41 loop : -0.75 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 33 HIS 0.005 0.001 HIS H 82 PHE 0.017 0.002 PHE L 62 TYR 0.020 0.002 TYR H 83 ARG 0.007 0.001 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8735 (tttm) REVERT: D 68 ASP cc_start: 0.8528 (t70) cc_final: 0.8221 (t0) REVERT: G 36 LYS cc_start: 0.8785 (mptt) cc_final: 0.8398 (mttm) REVERT: G 73 ASN cc_start: 0.8483 (OUTLIER) cc_final: 0.8278 (t0) REVERT: H 42 TYR cc_start: 0.8642 (t80) cc_final: 0.8291 (t80) REVERT: H 120 LYS cc_start: 0.9227 (ttpt) cc_final: 0.8983 (ttpt) REVERT: K 56 ARG cc_start: 0.7122 (ppt170) cc_final: 0.6869 (ppt170) REVERT: L 9 GLU cc_start: 0.6488 (tt0) cc_final: 0.6253 (tt0) REVERT: L 147 MET cc_start: 0.4154 (mpp) cc_final: 0.3613 (mpp) outliers start: 23 outliers final: 16 residues processed: 195 average time/residue: 0.3581 time to fit residues: 94.7141 Evaluate side-chains 184 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.0170 chunk 124 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15483 Z= 0.206 Angle : 0.577 12.031 22182 Z= 0.327 Chirality : 0.034 0.150 2516 Planarity : 0.004 0.036 1795 Dihedral : 28.958 179.647 4412 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.49 % Allowed : 15.68 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.85 (0.26), residues: 1058 helix: 2.30 (0.21), residues: 649 sheet: 0.66 (0.86), residues: 36 loop : -0.69 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 33 HIS 0.003 0.000 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR H 83 ARG 0.010 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8608 (m-10) cc_final: 0.8095 (m-10) REVERT: C 95 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8713 (tttm) REVERT: D 68 ASP cc_start: 0.8375 (t70) cc_final: 0.8119 (t0) REVERT: E 125 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7343 (mt0) REVERT: G 36 LYS cc_start: 0.8737 (mptt) cc_final: 0.8387 (mttm) REVERT: G 89 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8775 (t0) REVERT: H 33 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6438 (mtm180) REVERT: H 42 TYR cc_start: 0.8570 (t80) cc_final: 0.8232 (t80) REVERT: H 120 LYS cc_start: 0.9186 (ttpt) cc_final: 0.8956 (ttpt) REVERT: K 56 ARG cc_start: 0.6962 (ppt170) cc_final: 0.6716 (ppt170) REVERT: L 9 GLU cc_start: 0.6595 (tt0) cc_final: 0.6083 (tt0) REVERT: L 69 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5778 (m-10) REVERT: L 109 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (tt) REVERT: L 147 MET cc_start: 0.4247 (mpp) cc_final: 0.3640 (mpp) outliers start: 23 outliers final: 15 residues processed: 195 average time/residue: 0.3666 time to fit residues: 98.5814 Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15483 Z= 0.269 Angle : 0.599 12.711 22182 Z= 0.338 Chirality : 0.036 0.209 2516 Planarity : 0.004 0.038 1795 Dihedral : 29.062 179.017 4412 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.14 % Allowed : 17.08 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.75 (0.26), residues: 1058 helix: 2.19 (0.21), residues: 650 sheet: 0.96 (0.85), residues: 41 loop : -0.72 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.016 0.001 PHE L 62 TYR 0.018 0.002 TYR H 83 ARG 0.010 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8640 (m-10) cc_final: 0.8395 (m-80) REVERT: C 95 LYS cc_start: 0.8978 (ttmt) cc_final: 0.8722 (tttm) REVERT: E 125 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7393 (mt0) REVERT: G 36 LYS cc_start: 0.8765 (mptt) cc_final: 0.8394 (mttm) REVERT: G 89 ASN cc_start: 0.9348 (OUTLIER) cc_final: 0.8830 (t0) REVERT: H 33 ARG cc_start: 0.6846 (mtm180) cc_final: 0.6453 (mtm180) REVERT: H 42 TYR cc_start: 0.8631 (t80) cc_final: 0.8317 (t80) REVERT: H 120 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8949 (ttpt) REVERT: L 9 GLU cc_start: 0.6874 (tt0) cc_final: 0.6294 (tt0) REVERT: L 69 PHE cc_start: 0.6818 (OUTLIER) cc_final: 0.5884 (m-10) REVERT: L 109 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8207 (tt) REVERT: L 147 MET cc_start: 0.3863 (mpp) cc_final: 0.3120 (mpp) outliers start: 29 outliers final: 21 residues processed: 196 average time/residue: 0.3469 time to fit residues: 93.0948 Evaluate side-chains 199 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15483 Z= 0.227 Angle : 0.591 13.310 22182 Z= 0.331 Chirality : 0.035 0.224 2516 Planarity : 0.004 0.036 1795 Dihedral : 29.038 179.548 4412 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.03 % Allowed : 18.59 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.80 (0.26), residues: 1058 helix: 2.22 (0.21), residues: 650 sheet: 1.06 (0.85), residues: 41 loop : -0.71 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 77 HIS 0.003 0.001 HIS F 75 PHE 0.018 0.001 PHE L 62 TYR 0.014 0.001 TYR H 83 ARG 0.007 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9042 (mttm) cc_final: 0.8417 (mttm) REVERT: B 88 TYR cc_start: 0.8642 (m-10) cc_final: 0.8359 (m-80) REVERT: C 95 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8710 (tttm) REVERT: E 125 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: G 36 LYS cc_start: 0.8753 (mptt) cc_final: 0.8379 (mttm) REVERT: G 89 ASN cc_start: 0.9284 (OUTLIER) cc_final: 0.8807 (t0) REVERT: H 33 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6415 (mtm180) REVERT: H 42 TYR cc_start: 0.8597 (t80) cc_final: 0.8270 (t80) REVERT: H 120 LYS cc_start: 0.9206 (ttpt) cc_final: 0.8934 (ttpt) REVERT: K 20 MET cc_start: 0.7220 (mmm) cc_final: 0.6091 (mmt) REVERT: L 9 GLU cc_start: 0.6859 (tt0) cc_final: 0.6169 (tt0) REVERT: L 69 PHE cc_start: 0.6771 (OUTLIER) cc_final: 0.5886 (m-10) REVERT: L 109 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (tt) REVERT: L 147 MET cc_start: 0.3829 (mpp) cc_final: 0.3059 (mpp) outliers start: 28 outliers final: 20 residues processed: 195 average time/residue: 0.3278 time to fit residues: 87.3309 Evaluate side-chains 198 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15483 Z= 0.198 Angle : 0.577 13.640 22182 Z= 0.324 Chirality : 0.034 0.227 2516 Planarity : 0.004 0.046 1795 Dihedral : 28.994 179.697 4412 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 19.14 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.85 (0.26), residues: 1058 helix: 2.27 (0.21), residues: 651 sheet: 0.59 (0.86), residues: 36 loop : -0.63 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 33 HIS 0.003 0.000 HIS F 75 PHE 0.020 0.001 PHE L 62 TYR 0.014 0.001 TYR H 83 ARG 0.010 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9049 (mttm) cc_final: 0.8415 (mttm) REVERT: C 95 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8701 (tttm) REVERT: D 40 TYR cc_start: 0.9412 (m-80) cc_final: 0.9126 (m-80) REVERT: E 125 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: G 36 LYS cc_start: 0.8758 (mptt) cc_final: 0.8370 (mttm) REVERT: G 89 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.8741 (t0) REVERT: H 33 ARG cc_start: 0.6809 (mtm180) cc_final: 0.6462 (mtm180) REVERT: H 42 TYR cc_start: 0.8589 (t80) cc_final: 0.8249 (t80) REVERT: H 120 LYS cc_start: 0.9187 (ttpt) cc_final: 0.8921 (ttpt) REVERT: K 20 MET cc_start: 0.7221 (mmm) cc_final: 0.5976 (mmt) REVERT: L 9 GLU cc_start: 0.6747 (tt0) cc_final: 0.5823 (tt0) REVERT: L 69 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.5836 (m-10) REVERT: L 109 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8195 (tt) REVERT: L 147 MET cc_start: 0.4053 (mpp) cc_final: 0.3278 (mpp) outliers start: 25 outliers final: 17 residues processed: 200 average time/residue: 0.3578 time to fit residues: 97.1335 Evaluate side-chains 201 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN G 89 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15483 Z= 0.337 Angle : 0.644 13.545 22182 Z= 0.357 Chirality : 0.038 0.351 2516 Planarity : 0.005 0.042 1795 Dihedral : 29.188 179.049 4412 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.49 % Allowed : 19.89 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.55 (0.26), residues: 1058 helix: 1.98 (0.21), residues: 652 sheet: 0.78 (0.83), residues: 42 loop : -0.71 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 33 HIS 0.004 0.001 HIS H 82 PHE 0.016 0.002 PHE L 62 TYR 0.017 0.002 TYR H 83 ARG 0.012 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9029 (mttm) cc_final: 0.8404 (mttm) REVERT: C 95 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8717 (tttm) REVERT: D 40 TYR cc_start: 0.9455 (m-80) cc_final: 0.9200 (m-80) REVERT: E 125 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: G 36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8378 (mttm) REVERT: H 33 ARG cc_start: 0.6828 (mtm180) cc_final: 0.6433 (mtm180) REVERT: H 120 LYS cc_start: 0.9225 (ttpt) cc_final: 0.8930 (ttpt) REVERT: K 56 ARG cc_start: 0.6978 (ppt170) cc_final: 0.6570 (ppt170) REVERT: L 9 GLU cc_start: 0.6559 (tt0) cc_final: 0.5714 (tt0) REVERT: L 69 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5868 (m-10) REVERT: L 109 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8216 (tt) REVERT: L 147 MET cc_start: 0.4390 (mpp) cc_final: 0.3646 (mpp) outliers start: 23 outliers final: 19 residues processed: 186 average time/residue: 0.3438 time to fit residues: 87.9054 Evaluate side-chains 190 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 30.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 15483 Z= 0.420 Angle : 0.685 14.066 22182 Z= 0.378 Chirality : 0.040 0.315 2516 Planarity : 0.005 0.049 1795 Dihedral : 29.318 179.339 4412 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.59 % Allowed : 19.68 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.38 (0.26), residues: 1058 helix: 1.89 (0.21), residues: 646 sheet: 0.83 (0.82), residues: 42 loop : -0.84 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP L 33 HIS 0.005 0.001 HIS H 82 PHE 0.039 0.002 PHE L 62 TYR 0.020 0.002 TYR H 83 ARG 0.010 0.001 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9023 (mttm) cc_final: 0.8398 (mttm) REVERT: C 95 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8727 (tttm) REVERT: D 40 TYR cc_start: 0.9476 (m-80) cc_final: 0.9239 (m-80) REVERT: E 125 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7505 (mt0) REVERT: G 36 LYS cc_start: 0.8754 (mptt) cc_final: 0.8389 (mttm) REVERT: H 33 ARG cc_start: 0.6843 (mtm180) cc_final: 0.6476 (mtm180) REVERT: H 42 TYR cc_start: 0.8655 (t80) cc_final: 0.8373 (t80) REVERT: H 120 LYS cc_start: 0.9232 (ttpt) cc_final: 0.8927 (ttpt) REVERT: K 20 MET cc_start: 0.7526 (mmm) cc_final: 0.6533 (mmm) REVERT: K 46 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7627 (ptpt) REVERT: K 56 ARG cc_start: 0.6962 (ppt170) cc_final: 0.6373 (ppt170) REVERT: L 9 GLU cc_start: 0.6523 (tt0) cc_final: 0.5627 (tt0) REVERT: L 69 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5936 (m-10) REVERT: L 109 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8139 (tt) REVERT: L 147 MET cc_start: 0.4217 (mpp) cc_final: 0.3487 (mpp) outliers start: 24 outliers final: 21 residues processed: 184 average time/residue: 0.3532 time to fit residues: 88.3023 Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 93 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15483 Z= 0.261 Angle : 0.640 14.100 22182 Z= 0.353 Chirality : 0.037 0.359 2516 Planarity : 0.004 0.052 1795 Dihedral : 29.181 179.782 4412 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.05 % Allowed : 21.19 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.56 (0.26), residues: 1058 helix: 2.06 (0.21), residues: 645 sheet: 0.79 (0.82), residues: 42 loop : -0.80 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 33 HIS 0.003 0.001 HIS F 75 PHE 0.033 0.001 PHE L 62 TYR 0.021 0.002 TYR D 83 ARG 0.012 0.000 ARG L 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9043 (mttm) cc_final: 0.8400 (mttm) REVERT: C 95 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8737 (tttm) REVERT: D 40 TYR cc_start: 0.9433 (m-80) cc_final: 0.9214 (m-80) REVERT: D 71 GLU cc_start: 0.7913 (tp30) cc_final: 0.7546 (tp30) REVERT: E 125 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7446 (mt0) REVERT: G 36 LYS cc_start: 0.8740 (mptt) cc_final: 0.8374 (mttp) REVERT: H 33 ARG cc_start: 0.6783 (mtm180) cc_final: 0.6417 (mtm180) REVERT: H 42 TYR cc_start: 0.8595 (t80) cc_final: 0.8327 (t80) REVERT: H 57 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8195 (mmmm) REVERT: H 120 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8919 (ttpt) REVERT: K 20 MET cc_start: 0.7486 (mmm) cc_final: 0.6518 (mmm) REVERT: K 46 LYS cc_start: 0.7841 (ptpt) cc_final: 0.7572 (ptpt) REVERT: K 56 ARG cc_start: 0.6822 (ppt170) cc_final: 0.6249 (ppt170) REVERT: L 9 GLU cc_start: 0.6453 (tt0) cc_final: 0.5526 (tt0) REVERT: L 69 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.5885 (m-10) REVERT: L 109 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8206 (tt) REVERT: L 147 MET cc_start: 0.4318 (mpp) cc_final: 0.3604 (mpp) outliers start: 19 outliers final: 16 residues processed: 190 average time/residue: 0.3507 time to fit residues: 90.7527 Evaluate side-chains 194 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.0020 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN D 95 GLN K 73 ASN L 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.146595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106154 restraints weight = 26441.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104797 restraints weight = 47164.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.105523 restraints weight = 46523.844| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15483 Z= 0.184 Angle : 0.619 14.671 22182 Z= 0.342 Chirality : 0.036 0.391 2516 Planarity : 0.004 0.036 1795 Dihedral : 29.033 179.916 4412 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 21.51 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.72 (0.26), residues: 1058 helix: 2.21 (0.21), residues: 649 sheet: 0.48 (0.85), residues: 37 loop : -0.74 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 77 HIS 0.004 0.001 HIS F 75 PHE 0.027 0.001 PHE L 62 TYR 0.029 0.002 TYR D 83 ARG 0.011 0.000 ARG L 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2657.14 seconds wall clock time: 57 minutes 52.68 seconds (3472.68 seconds total)