Starting phenix.real_space_refine on Sun Nov 17 11:44:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn2_40610/11_2024/8sn2_40610.cif" } resolution = 3.6 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= 0.071 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 32 5.16 5 C 7886 2.51 5 N 2607 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 13992 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: "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: 821 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Conformer: "B" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} bond proxies already assigned to first conformer: 820 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: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} 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: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 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: "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 12290 SG CYS K 31 75.714 52.537 66.546 1.00 43.01 S ATOM 12440 SG CYS K 51 76.545 50.797 63.302 1.00 44.84 S ATOM 12464 SG CYS K 54 74.977 48.802 66.187 1.00 44.65 S ATOM 12181 SG CYS K 16 84.103 56.800 57.767 1.00 44.32 S ATOM 12199 SG CYS K 19 86.199 57.014 54.674 1.00 41.66 S ATOM 12329 SG CYS K 36 83.580 59.855 55.726 1.00 45.57 S ATOM 12351 SG CYS K 39 82.441 56.789 54.183 1.00 43.08 S Time building chain proxies: 9.18, per 1000 atoms: 0.66 Number of scatterers: 13992 At special positions: 0 Unit cell: (108.896, 132.8, 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 32 16.00 P 294 15.00 O 3171 8.00 N 2607 7.00 C 7886 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: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " 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 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " Number of angles added : 9 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 11 sheets defined 65.5% alpha, 4.1% beta 135 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 6.15 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.922A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 3.554A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.563A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.866A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.989A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.513A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.783A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.527A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.526A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.763A pdb=" N ILE D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.504A 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 removed outlier: 3.600A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.978A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.139A 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 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.778A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.888A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 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 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.532A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.526A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.774A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 4.434A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 4.157A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.621A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (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 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.930A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.735A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.946A 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 removed outlier: 3.519A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 7.924A 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 'C' and resid 101 through 102 removed outlier: 6.879A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.402A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.667A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 25 469 hydrogen bonds defined for protein. 1391 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3379 1.34 - 1.46: 4208 1.46 - 1.58: 6637 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14857 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.61e+00 bond pdb=" N LYS L 63 " pdb=" CA LYS L 63 " ideal model delta sigma weight residual 1.456 1.472 -0.016 1.55e-02 4.16e+03 1.12e+00 bond pdb=" C PHE L 62 " pdb=" N LYS L 63 " ideal model delta sigma weight residual 1.331 1.352 -0.021 2.07e-02 2.33e+03 1.06e+00 bond pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.27e-01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 9.15e-01 ... (remaining 14852 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20633 1.29 - 2.59: 629 2.59 - 3.88: 59 3.88 - 5.17: 18 5.17 - 6.47: 4 Bond angle restraints: 21343 Sorted by residual: angle pdb=" CA LYS K 46 " pdb=" CB LYS K 46 " pdb=" CG LYS K 46 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.65e+00 angle pdb=" CA ARG L 136 " pdb=" CB ARG L 136 " pdb=" CG ARG L 136 " ideal model delta sigma weight residual 114.10 118.58 -4.48 2.00e+00 2.50e-01 5.02e+00 angle pdb=" CA GLU K 25 " pdb=" CB GLU K 25 " pdb=" CG GLU K 25 " ideal model delta sigma weight residual 114.10 118.57 -4.47 2.00e+00 2.50e-01 4.98e+00 angle pdb=" CB MET B 84 " pdb=" CG MET B 84 " pdb=" SD MET B 84 " ideal model delta sigma weight residual 112.70 119.17 -6.47 3.00e+00 1.11e-01 4.65e+00 angle pdb=" CA ASN G 110 " pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 112.60 114.63 -2.03 1.00e+00 1.00e+00 4.11e+00 ... (remaining 21338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 6880 35.27 - 70.55: 1320 70.55 - 105.82: 14 105.82 - 141.09: 0 141.09 - 176.36: 2 Dihedral angle restraints: 8216 sinusoidal: 5298 harmonic: 2918 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 220.00 43.64 176.36 1 3.50e+01 8.16e-04 1.57e+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 75.49 144.51 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA PHE L 62 " pdb=" C PHE L 62 " pdb=" N LYS L 63 " pdb=" CA LYS L 63 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 8213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1761 0.031 - 0.062: 497 0.062 - 0.093: 100 0.093 - 0.123: 53 0.123 - 0.154: 7 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CB ILE D 94 " pdb=" CA ILE D 94 " pdb=" CG1 ILE D 94 " pdb=" CG2 ILE D 94 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.95e-01 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2415 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 42 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO E 43 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 43 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 43 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.009 2.00e-02 2.50e+03 1.27e-02 3.23e+00 pdb=" CG TYR D 83 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 60 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO L 61 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO L 61 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 61 " 0.022 5.00e-02 4.00e+02 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1804 2.76 - 3.47: 18753 3.47 - 4.19: 36695 4.19 - 4.90: 57297 Nonbonded interactions: 114551 Sorted by model distance: nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" OG SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.058 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.175 2.496 nonbonded pdb=" O PRO L 61 " pdb=" NE1 TRP L 93 " model vdw 2.193 3.120 ... (remaining 114546 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' and (resid 37 through 55 or resid 57 through 135)) selection = (chain 'E' and (resid 37 through 55 or resid 57 through 135)) } 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 123) selection = chain 'H' } 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=0.17 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: 0.790 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: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.130 Find NCS groups from input model: 0.380 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 0.038 14857 Z= 0.161 Angle : 0.530 6.469 21343 Z= 0.313 Chirality : 0.033 0.154 2418 Planarity : 0.004 0.048 1687 Dihedral : 25.924 176.363 6330 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 2.22 (0.27), residues: 982 helix: 2.71 (0.22), residues: 612 sheet: 0.72 (0.87), residues: 29 loop : -0.86 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 77 HIS 0.005 0.001 HIS G 82 PHE 0.009 0.001 PHE L 62 TYR 0.031 0.001 TYR D 83 ARG 0.007 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8738 (mtpp) cc_final: 0.8388 (mttp) REVERT: C 41 GLU cc_start: 0.7306 (tt0) cc_final: 0.7102 (tt0) REVERT: D 71 GLU cc_start: 0.8317 (tp30) cc_final: 0.8086 (tp30) REVERT: F 25 ASN cc_start: 0.7791 (m110) cc_final: 0.7430 (m-40) REVERT: H 59 MET cc_start: 0.8622 (tpp) cc_final: 0.8399 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3241 time to fit residues: 83.2376 Evaluate side-chains 141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14857 Z= 0.237 Angle : 0.568 6.828 21343 Z= 0.331 Chirality : 0.035 0.151 2418 Planarity : 0.004 0.042 1687 Dihedral : 29.298 175.623 4330 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.29 % Allowed : 9.94 % Favored : 88.77 % 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: 1.99 (0.27), residues: 982 helix: 2.58 (0.21), residues: 629 sheet: 0.43 (0.93), residues: 30 loop : -1.28 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 77 HIS 0.003 0.001 HIS G 31 PHE 0.011 0.001 PHE E 67 TYR 0.016 0.002 TYR H 83 ARG 0.004 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 145 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8983 (t70) cc_final: 0.8763 (t0) REVERT: C 36 LYS cc_start: 0.8768 (mtpp) cc_final: 0.8543 (mttp) REVERT: D 71 GLU cc_start: 0.8451 (tp30) cc_final: 0.8188 (tp30) REVERT: F 25 ASN cc_start: 0.7830 (m110) cc_final: 0.7508 (m-40) outliers start: 11 outliers final: 9 residues processed: 149 average time/residue: 0.2913 time to fit residues: 62.3446 Evaluate side-chains 149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN D 49 HIS F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14857 Z= 0.418 Angle : 0.673 6.848 21343 Z= 0.387 Chirality : 0.041 0.210 2418 Planarity : 0.005 0.041 1687 Dihedral : 30.216 170.747 4330 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.46 % Allowed : 11.58 % Favored : 85.96 % 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: 1.39 (0.27), residues: 982 helix: 2.23 (0.21), residues: 616 sheet: 0.26 (0.92), residues: 30 loop : -1.62 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP L 93 HIS 0.006 0.001 HIS G 31 PHE 0.012 0.002 PHE D 65 TYR 0.020 0.002 TYR D 121 ARG 0.003 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8991 (t70) cc_final: 0.8754 (t0) REVERT: B 98 TYR cc_start: 0.8770 (m-10) cc_final: 0.8435 (m-10) REVERT: C 36 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8433 (mttm) REVERT: F 25 ASN cc_start: 0.7946 (m110) cc_final: 0.7676 (m-40) REVERT: H 59 MET cc_start: 0.9088 (tpp) cc_final: 0.8671 (tpp) REVERT: H 80 LEU cc_start: 0.9344 (tp) cc_final: 0.9096 (tp) REVERT: K 63 ARG cc_start: 0.9030 (ttp80) cc_final: 0.8728 (ttp-170) REVERT: L 1 MET cc_start: 0.7232 (ppp) cc_final: 0.6989 (pmm) outliers start: 21 outliers final: 18 residues processed: 145 average time/residue: 0.2939 time to fit residues: 60.3431 Evaluate side-chains 139 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 SER 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 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 80 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.0470 chunk 52 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14857 Z= 0.186 Angle : 0.549 5.745 21343 Z= 0.324 Chirality : 0.034 0.176 2418 Planarity : 0.004 0.044 1687 Dihedral : 29.645 173.187 4330 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.87 % Allowed : 13.57 % Favored : 84.56 % 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: 1.93 (0.27), residues: 982 helix: 2.62 (0.21), residues: 623 sheet: 0.35 (0.93), residues: 30 loop : -1.41 (0.30), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 93 HIS 0.007 0.001 HIS C 31 PHE 0.010 0.001 PHE E 67 TYR 0.016 0.001 TYR D 83 ARG 0.006 0.000 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8940 (t70) cc_final: 0.8704 (t0) REVERT: B 98 TYR cc_start: 0.8727 (m-10) cc_final: 0.8434 (m-10) REVERT: C 36 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8451 (mttp) REVERT: D 71 GLU cc_start: 0.8510 (tp30) cc_final: 0.8260 (tp30) REVERT: F 25 ASN cc_start: 0.7874 (m110) cc_final: 0.7563 (m-40) REVERT: H 59 MET cc_start: 0.8839 (tpp) cc_final: 0.8187 (tpp) REVERT: L 11 SER cc_start: 0.7112 (p) cc_final: 0.6747 (t) outliers start: 16 outliers final: 11 residues processed: 145 average time/residue: 0.2805 time to fit residues: 58.6291 Evaluate side-chains 142 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 38 ASN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14857 Z= 0.185 Angle : 0.548 12.476 21343 Z= 0.319 Chirality : 0.034 0.153 2418 Planarity : 0.004 0.039 1687 Dihedral : 29.548 174.152 4330 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.22 % Allowed : 14.04 % Favored : 83.74 % 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: 2.10 (0.27), residues: 982 helix: 2.72 (0.21), residues: 623 sheet: 0.53 (0.97), residues: 30 loop : -1.28 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 93 HIS 0.004 0.001 HIS K 65 PHE 0.009 0.001 PHE E 67 TYR 0.009 0.001 TYR H 83 ARG 0.006 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8945 (t70) cc_final: 0.8706 (t0) REVERT: B 98 TYR cc_start: 0.8676 (m-10) cc_final: 0.8393 (m-10) REVERT: C 36 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8448 (mttp) REVERT: D 71 GLU cc_start: 0.8531 (tp30) cc_final: 0.8265 (tp30) REVERT: F 25 ASN cc_start: 0.7872 (m110) cc_final: 0.7596 (m-40) REVERT: K 64 TYR cc_start: 0.8196 (t80) cc_final: 0.7667 (t80) REVERT: L 11 SER cc_start: 0.7006 (p) cc_final: 0.6602 (t) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.2749 time to fit residues: 58.6937 Evaluate side-chains 141 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 123 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14857 Z= 0.182 Angle : 0.550 11.660 21343 Z= 0.319 Chirality : 0.034 0.228 2418 Planarity : 0.004 0.038 1687 Dihedral : 29.442 174.816 4330 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.11 % Allowed : 14.97 % Favored : 82.92 % 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: 2.15 (0.27), residues: 982 helix: 2.77 (0.21), residues: 623 sheet: 0.38 (0.96), residues: 30 loop : -1.27 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 93 HIS 0.006 0.001 HIS C 31 PHE 0.010 0.001 PHE L 51 TYR 0.011 0.001 TYR H 83 ARG 0.007 0.000 ARG K 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8950 (t70) cc_final: 0.8701 (t0) REVERT: B 98 TYR cc_start: 0.8677 (m-10) cc_final: 0.8413 (m-10) REVERT: C 36 LYS cc_start: 0.8773 (mtpp) cc_final: 0.8500 (mttp) REVERT: D 71 GLU cc_start: 0.8529 (tp30) cc_final: 0.8268 (tp30) REVERT: F 25 ASN cc_start: 0.7881 (m110) cc_final: 0.7577 (m-40) REVERT: L 11 SER cc_start: 0.7139 (p) cc_final: 0.6756 (t) outliers start: 18 outliers final: 15 residues processed: 143 average time/residue: 0.2864 time to fit residues: 58.8387 Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 123 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 38 ASN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14857 Z= 0.221 Angle : 0.562 11.707 21343 Z= 0.325 Chirality : 0.035 0.224 2418 Planarity : 0.004 0.037 1687 Dihedral : 29.499 174.510 4330 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.46 % Allowed : 15.20 % Favored : 82.34 % 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: 2.07 (0.27), residues: 982 helix: 2.69 (0.21), residues: 623 sheet: 0.34 (0.96), residues: 30 loop : -1.26 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 93 HIS 0.004 0.001 HIS K 65 PHE 0.010 0.001 PHE L 51 TYR 0.016 0.001 TYR H 83 ARG 0.005 0.000 ARG K 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8971 (t70) cc_final: 0.8721 (t0) REVERT: B 98 TYR cc_start: 0.8694 (m-10) cc_final: 0.8414 (m-10) REVERT: C 36 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8545 (mttp) REVERT: D 71 GLU cc_start: 0.8497 (tp30) cc_final: 0.8177 (tp30) REVERT: F 25 ASN cc_start: 0.7903 (m110) cc_final: 0.7605 (m-40) REVERT: H 59 MET cc_start: 0.8725 (tpp) cc_final: 0.8291 (tpp) REVERT: L 11 SER cc_start: 0.7034 (p) cc_final: 0.6620 (t) outliers start: 21 outliers final: 20 residues processed: 141 average time/residue: 0.2834 time to fit residues: 56.8932 Evaluate side-chains 152 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 123 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14857 Z= 0.284 Angle : 0.603 11.658 21343 Z= 0.347 Chirality : 0.037 0.236 2418 Planarity : 0.004 0.040 1687 Dihedral : 29.735 172.649 4330 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.46 % Allowed : 15.91 % Favored : 81.64 % 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: 1.83 (0.27), residues: 982 helix: 2.56 (0.21), residues: 621 sheet: 0.15 (0.94), residues: 30 loop : -1.45 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 93 HIS 0.004 0.001 HIS C 31 PHE 0.009 0.001 PHE D 65 TYR 0.021 0.002 TYR H 83 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8998 (t70) cc_final: 0.8795 (t0) REVERT: B 98 TYR cc_start: 0.8754 (m-10) cc_final: 0.8538 (m-10) REVERT: C 36 LYS cc_start: 0.8814 (mtpp) cc_final: 0.8539 (mttp) REVERT: F 25 ASN cc_start: 0.7938 (m110) cc_final: 0.7642 (m-40) REVERT: H 59 MET cc_start: 0.8870 (tpp) cc_final: 0.8329 (tpp) REVERT: K 63 ARG cc_start: 0.9066 (ttp80) cc_final: 0.8668 (ttp-170) REVERT: L 11 SER cc_start: 0.6949 (p) cc_final: 0.6526 (t) outliers start: 21 outliers final: 17 residues processed: 145 average time/residue: 0.2838 time to fit residues: 58.5270 Evaluate side-chains 149 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14857 Z= 0.377 Angle : 0.658 15.907 21343 Z= 0.375 Chirality : 0.039 0.225 2418 Planarity : 0.005 0.042 1687 Dihedral : 30.048 171.660 4330 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.34 % Allowed : 16.49 % Favored : 81.17 % 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: 1.51 (0.27), residues: 982 helix: 2.33 (0.21), residues: 622 sheet: -0.33 (0.90), residues: 30 loop : -1.60 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 93 HIS 0.004 0.001 HIS G 31 PHE 0.012 0.002 PHE D 65 TYR 0.030 0.002 TYR H 83 ARG 0.005 0.000 ARG K 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.9010 (t70) cc_final: 0.8707 (t0) REVERT: B 98 TYR cc_start: 0.8762 (m-10) cc_final: 0.8542 (m-10) REVERT: C 36 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8460 (mttm) REVERT: F 25 ASN cc_start: 0.8029 (m110) cc_final: 0.7743 (m-40) REVERT: H 59 MET cc_start: 0.8916 (tpp) cc_final: 0.8515 (tpp) REVERT: K 63 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8642 (ttp-170) outliers start: 20 outliers final: 17 residues processed: 136 average time/residue: 0.2907 time to fit residues: 56.6118 Evaluate side-chains 136 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14857 Z= 0.287 Angle : 0.620 16.350 21343 Z= 0.354 Chirality : 0.037 0.247 2418 Planarity : 0.005 0.048 1687 Dihedral : 29.881 172.645 4330 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.87 % Allowed : 17.43 % Favored : 80.70 % 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: 1.58 (0.27), residues: 982 helix: 2.40 (0.21), residues: 622 sheet: -0.45 (0.90), residues: 30 loop : -1.60 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 93 HIS 0.004 0.001 HIS G 31 PHE 0.010 0.001 PHE L 51 TYR 0.025 0.002 TYR H 83 ARG 0.004 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1964 Ramachandran restraints generated. 982 Oldfield, 0 Emsley, 982 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 ASP cc_start: 0.8999 (t70) cc_final: 0.8707 (t0) REVERT: B 98 TYR cc_start: 0.8738 (m-10) cc_final: 0.8520 (m-10) REVERT: C 36 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8435 (mttm) REVERT: F 25 ASN cc_start: 0.8009 (m110) cc_final: 0.7720 (m-40) REVERT: H 59 MET cc_start: 0.8852 (tpp) cc_final: 0.8432 (tpp) REVERT: K 63 ARG cc_start: 0.9069 (ttp80) cc_final: 0.8679 (ttp-170) REVERT: L 11 SER cc_start: 0.6796 (p) cc_final: 0.6382 (t) outliers start: 16 outliers final: 15 residues processed: 140 average time/residue: 0.2781 time to fit residues: 56.0390 Evaluate side-chains 146 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 6 ILE Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain L residue 100 SER Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN L 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.098772 restraints weight = 29491.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100413 restraints weight = 21230.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.100657 restraints weight = 13451.848| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14857 Z= 0.255 Angle : 0.605 16.206 21343 Z= 0.346 Chirality : 0.036 0.233 2418 Planarity : 0.005 0.059 1687 Dihedral : 29.789 173.348 4330 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.87 % Allowed : 17.66 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.27), residues: 982 helix: 2.47 (0.21), residues: 622 sheet: -0.35 (0.93), residues: 30 loop : -1.53 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 93 HIS 0.004 0.001 HIS K 65 PHE 0.009 0.001 PHE L 51 TYR 0.059 0.002 TYR K 84 ARG 0.004 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.51 seconds wall clock time: 41 minutes 46.55 seconds (2506.55 seconds total)