Starting phenix.real_space_refine on Wed Jun 11 16:28:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.map" model { file = "/net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dgg_46823/06_2025/9dgg_46823.cif" } resolution = 2.98 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= 0.009 sd= 0.052 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 4 6.06 5 P 286 5.49 5 S 30 5.16 5 C 7498 2.51 5 N 2473 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13339 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 647 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 81} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2948 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "J" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2915 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain: "K" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 773 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 95} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "L" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 757 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 93} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 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} Chain: "L" 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 11922 SG CYS K 18 25.021 51.829 54.507 1.00135.22 S ATOM 11943 SG CYS K 21 21.745 50.037 54.263 1.00124.42 S ATOM 12081 SG CYS K 39 23.963 49.309 57.216 1.00130.53 S ATOM 12103 SG CYS K 42 24.962 48.085 53.730 1.00120.87 S ATOM 12040 SG CYS K 34 36.111 58.907 54.236 1.00114.18 S ATOM 12184 SG CYS K 53 33.577 58.092 51.442 1.00122.85 S ATOM 12205 SG CYS K 56 34.973 61.605 51.773 1.00126.03 S ATOM 12839 SG CYS L 51 36.841 63.352 77.033 1.00131.51 S ATOM 12860 SG CYS L 54 35.221 66.064 79.034 1.00126.05 S ATOM 13004 SG CYS L 72 35.238 66.138 75.239 1.00129.09 S ATOM 13023 SG CYS L 75 38.438 66.933 77.192 1.00119.18 S ATOM 12958 SG CYS L 67 41.328 54.065 69.566 1.00118.73 S ATOM 13112 SG CYS L 87 42.526 55.196 73.032 1.00136.41 S ATOM 13132 SG CYS L 90 42.913 51.478 71.966 1.00125.62 S Time building chain proxies: 7.89, per 1000 atoms: 0.59 Number of scatterers: 13339 At special positions: 0 Unit cell: (110.696, 116.176, 124.944, 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 4 29.99 S 30 16.00 P 286 15.00 O 3048 8.00 N 2473 7.00 C 7498 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: 3.12 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " Number of angles added : 18 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1814 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 13 sheets defined 66.1% alpha, 4.3% beta 141 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.529A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.487A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 12 through 17 Processing helix chain 'K' and resid 40 through 48 removed outlier: 3.769A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'L' and resid 21 through 25 Processing helix chain 'L' and resid 45 through 50 Processing helix chain 'L' and resid 73 through 83 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.859A 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: 7.374A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (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: 6.878A 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: 6.664A 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 42 through 43 removed outlier: 7.548A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 5 through 8 Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AB4, first strand: chain 'L' and resid 70 through 72 473 hydrogen bonds defined for protein. 1377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 362 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 3.67 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: 3279 1.34 - 1.46: 4148 1.46 - 1.58: 6115 1.58 - 1.70: 570 1.70 - 1.82: 44 Bond restraints: 14156 Sorted by residual: bond pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.08e-02 8.57e+03 8.74e+00 bond pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.26e-02 6.30e+03 8.45e+00 bond pdb=" N VAL F 21 " pdb=" CA VAL F 21 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 bond pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.37e-02 5.33e+03 7.32e+00 bond pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.84e+00 ... (remaining 14151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 19761 1.66 - 3.31: 562 3.31 - 4.97: 41 4.97 - 6.63: 10 6.63 - 8.28: 5 Bond angle restraints: 20379 Sorted by residual: angle pdb=" N ASN G 73 " pdb=" CA ASN G 73 " pdb=" C ASN G 73 " ideal model delta sigma weight residual 114.39 107.00 7.39 1.45e+00 4.76e-01 2.60e+01 angle pdb=" C PRO L 102 " pdb=" N ASP L 103 " pdb=" CA ASP L 103 " ideal model delta sigma weight residual 123.30 117.63 5.67 1.44e+00 4.82e-01 1.55e+01 angle pdb=" N VAL B 21 " pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 112.96 109.10 3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" N GLN B 27 " pdb=" CA GLN B 27 " pdb=" C GLN B 27 " ideal model delta sigma weight residual 113.19 108.77 4.42 1.19e+00 7.06e-01 1.38e+01 angle pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" O LEU F 22 " ideal model delta sigma weight residual 121.56 118.07 3.49 1.09e+00 8.42e-01 1.02e+01 ... (remaining 20374 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 5863 26.97 - 53.94: 1631 53.94 - 80.91: 286 80.91 - 107.89: 2 107.89 - 134.86: 2 Dihedral angle restraints: 7784 sinusoidal: 4984 harmonic: 2800 Sorted by residual: dihedral pdb=" C4' DC I 128 " pdb=" C3' DC I 128 " pdb=" O3' DC I 128 " pdb=" P DT I 129 " ideal model delta sinusoidal sigma weight residual 220.00 85.14 134.86 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" C4' DC I 36 " pdb=" C3' DC I 36 " pdb=" O3' DC I 36 " pdb=" P DT I 37 " ideal model delta sinusoidal sigma weight residual 220.00 87.44 132.56 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" CG ARG B 95 " pdb=" CD ARG B 95 " pdb=" NE ARG B 95 " pdb=" CZ ARG B 95 " ideal model delta sinusoidal sigma weight residual -90.00 -42.02 -47.98 2 1.50e+01 4.44e-03 1.18e+01 ... (remaining 7781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2321 0.107 - 0.214: 26 0.214 - 0.321: 1 0.321 - 0.428: 0 0.428 - 0.535: 2 Chirality restraints: 2350 Sorted by residual: chirality pdb=" P DG J 152 " pdb=" OP1 DG J 152 " pdb=" OP2 DG J 152 " pdb=" O5' DG J 152 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" P DC I 36 " pdb=" OP1 DC I 36 " pdb=" OP2 DC I 36 " pdb=" O5' DC I 36 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.61e+00 chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2347 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.44e+00 pdb=" N PRO D 100 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 22 " -0.011 2.00e-02 2.50e+03 1.41e-02 3.96e+00 pdb=" CG TYR L 22 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR L 22 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR L 22 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR L 22 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR L 22 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 22 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 22 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 99 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO H 100 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO H 100 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 100 " -0.025 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2206 2.77 - 3.31: 12147 3.31 - 3.84: 26790 3.84 - 4.37: 30203 4.37 - 4.90: 44284 Nonbonded interactions: 115630 Sorted by model distance: nonbonded pdb=" OD1 ASP L 103 " pdb=" N PHE L 106 " model vdw 2.243 3.120 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.279 3.040 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.300 3.040 nonbonded pdb=" NH2 ARG K 93 " pdb=" OG1 THR L 27 " model vdw 2.302 3.120 ... (remaining 115625 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 20 through 21 and (name N or name CA or name C or name O \ or name CB )) or resid 22 or (resid 23 through 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 37.850 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 : 0.004 0.040 14172 Z= 0.184 Angle : 0.635 8.282 20397 Z= 0.384 Chirality : 0.040 0.535 2350 Planarity : 0.005 0.060 1587 Dihedral : 27.077 134.857 5970 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.26 % Allowed : 17.67 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.27), residues: 939 helix: 2.30 (0.20), residues: 617 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 17 HIS 0.005 0.001 HIS G 31 PHE 0.022 0.002 PHE K 87 TYR 0.034 0.002 TYR L 22 ARG 0.012 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.06112 ( 835) hydrogen bonds : angle 2.98110 ( 2097) metal coordination : bond 0.00733 ( 16) metal coordination : angle 2.14623 ( 18) covalent geometry : bond 0.00361 (14156) covalent geometry : angle 0.63199 (20379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 310 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 GLN cc_start: 0.9253 (mm-40) cc_final: 0.9038 (mm110) REVERT: C 104 GLN cc_start: 0.8957 (mm110) cc_final: 0.8754 (mm110) REVERT: D 39 TYR cc_start: 0.8604 (t80) cc_final: 0.8307 (t80) REVERT: D 42 LEU cc_start: 0.9575 (tp) cc_final: 0.9338 (tp) REVERT: D 112 THR cc_start: 0.9565 (m) cc_final: 0.9360 (p) REVERT: E 58 THR cc_start: 0.9595 (p) cc_final: 0.9306 (t) REVERT: F 88 TYR cc_start: 0.9249 (m-10) cc_final: 0.9017 (m-80) REVERT: G 62 ILE cc_start: 0.9698 (mm) cc_final: 0.9452 (tt) REVERT: G 90 ASP cc_start: 0.8474 (t70) cc_final: 0.8077 (t0) REVERT: H 80 TYR cc_start: 0.9196 (m-10) cc_final: 0.8521 (m-10) REVERT: H 102 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8306 (mm-30) REVERT: K 10 THR cc_start: 0.8704 (p) cc_final: 0.8501 (m) REVERT: K 74 THR cc_start: 0.9531 (m) cc_final: 0.8959 (p) REVERT: L 65 LYS cc_start: 0.8894 (mttt) cc_final: 0.7712 (mttm) REVERT: L 86 GLU cc_start: 0.8809 (pt0) cc_final: 0.8606 (pp20) REVERT: L 101 ARG cc_start: 0.8138 (mmt-90) cc_final: 0.7875 (mmt-90) REVERT: L 107 ASP cc_start: 0.9149 (m-30) cc_final: 0.8723 (m-30) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 1.2901 time to fit residues: 432.7763 Evaluate side-chains 237 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 110 ASN F 93 GLN G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.048951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.033977 restraints weight = 60895.840| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.27 r_work: 0.2457 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 14172 Z= 0.292 Angle : 0.622 7.545 20397 Z= 0.361 Chirality : 0.039 0.178 2350 Planarity : 0.005 0.044 1587 Dihedral : 29.794 127.693 4181 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.84 % Allowed : 27.27 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.27), residues: 939 helix: 2.43 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.15 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.002 PHE B 100 TYR 0.011 0.002 TYR C 57 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 835) hydrogen bonds : angle 3.02761 ( 2097) metal coordination : bond 0.02753 ( 16) metal coordination : angle 2.67879 ( 18) covalent geometry : bond 0.00653 (14156) covalent geometry : angle 0.61714 (20379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 236 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8748 (tpt-90) REVERT: C 39 TYR cc_start: 0.9493 (m-80) cc_final: 0.9243 (m-80) REVERT: C 72 ASP cc_start: 0.9421 (t0) cc_final: 0.9076 (m-30) REVERT: C 104 GLN cc_start: 0.9099 (mm110) cc_final: 0.8804 (mm110) REVERT: D 34 TYR cc_start: 0.9613 (m-80) cc_final: 0.9409 (m-80) REVERT: D 39 TYR cc_start: 0.8918 (t80) cc_final: 0.8690 (t80) REVERT: D 42 LEU cc_start: 0.9432 (tp) cc_final: 0.9164 (tp) REVERT: D 65 ASP cc_start: 0.9344 (t0) cc_final: 0.9119 (t0) REVERT: D 102 GLU cc_start: 0.9343 (tp30) cc_final: 0.8717 (tp30) REVERT: D 112 THR cc_start: 0.9682 (m) cc_final: 0.9380 (p) REVERT: E 59 GLU cc_start: 0.8957 (pm20) cc_final: 0.8709 (pm20) REVERT: E 73 GLU cc_start: 0.9090 (tt0) cc_final: 0.8798 (tt0) REVERT: E 94 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8919 (mm-30) REVERT: F 85 ASP cc_start: 0.9347 (m-30) cc_final: 0.9146 (m-30) REVERT: F 88 TYR cc_start: 0.9352 (m-10) cc_final: 0.9134 (m-80) REVERT: G 41 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8502 (tm-30) REVERT: G 62 ILE cc_start: 0.9631 (mm) cc_final: 0.9355 (tt) REVERT: G 90 ASP cc_start: 0.8498 (t70) cc_final: 0.7992 (t0) REVERT: H 65 ASP cc_start: 0.9494 (t0) cc_final: 0.9276 (t0) REVERT: H 80 TYR cc_start: 0.9235 (m-10) cc_final: 0.8744 (m-10) REVERT: H 102 GLU cc_start: 0.9215 (mm-30) cc_final: 0.8673 (mm-30) REVERT: K 27 ASP cc_start: 0.9150 (t0) cc_final: 0.8946 (t0) REVERT: K 69 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9248 (pp) REVERT: K 91 MET cc_start: 0.8681 (tpt) cc_final: 0.7549 (tpt) REVERT: L 23 GLU cc_start: 0.9431 (mt-10) cc_final: 0.9136 (pt0) REVERT: L 57 MET cc_start: 0.8135 (tmm) cc_final: 0.7897 (tmm) REVERT: L 62 MET cc_start: 0.9179 (mmm) cc_final: 0.8836 (mmm) REVERT: L 65 LYS cc_start: 0.8668 (mttt) cc_final: 0.8159 (mttp) REVERT: L 86 GLU cc_start: 0.9055 (pt0) cc_final: 0.8812 (pp20) REVERT: L 101 ARG cc_start: 0.8699 (mmt-90) cc_final: 0.7551 (mmt-90) REVERT: L 103 ASP cc_start: 0.8909 (t0) cc_final: 0.8282 (t0) REVERT: L 107 ASP cc_start: 0.9420 (m-30) cc_final: 0.8982 (m-30) outliers start: 30 outliers final: 17 residues processed: 249 average time/residue: 1.3519 time to fit residues: 364.0251 Evaluate side-chains 232 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 30 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** G 73 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.049826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.034955 restraints weight = 60550.447| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 2.26 r_work: 0.2497 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14172 Z= 0.172 Angle : 0.579 8.866 20397 Z= 0.336 Chirality : 0.035 0.187 2350 Planarity : 0.004 0.037 1587 Dihedral : 29.556 124.631 4181 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.33 % Allowed : 27.53 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 939 helix: 2.40 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -0.16 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP L 17 HIS 0.005 0.001 HIS K 15 PHE 0.010 0.001 PHE K 97 TYR 0.011 0.001 TYR C 57 ARG 0.009 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 835) hydrogen bonds : angle 2.90860 ( 2097) metal coordination : bond 0.01269 ( 16) metal coordination : angle 2.20260 ( 18) covalent geometry : bond 0.00382 (14156) covalent geometry : angle 0.57507 (20379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8811 (tt0) REVERT: A 129 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8821 (tpt90) REVERT: C 91 GLU cc_start: 0.9260 (tt0) cc_final: 0.8696 (tp30) REVERT: C 104 GLN cc_start: 0.9008 (mm110) cc_final: 0.8649 (mm110) REVERT: D 39 TYR cc_start: 0.8792 (t80) cc_final: 0.8583 (t80) REVERT: D 42 LEU cc_start: 0.9415 (tp) cc_final: 0.9169 (tp) REVERT: D 65 ASP cc_start: 0.9392 (t0) cc_final: 0.9087 (OUTLIER) REVERT: D 102 GLU cc_start: 0.9217 (tp30) cc_final: 0.8581 (tp30) REVERT: D 112 THR cc_start: 0.9674 (m) cc_final: 0.9362 (p) REVERT: E 59 GLU cc_start: 0.8955 (pm20) cc_final: 0.8559 (pm20) REVERT: E 73 GLU cc_start: 0.9038 (tt0) cc_final: 0.8750 (tt0) REVERT: E 94 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8861 (mm-30) REVERT: F 73 THR cc_start: 0.9701 (OUTLIER) cc_final: 0.9256 (p) REVERT: F 88 TYR cc_start: 0.9312 (m-10) cc_final: 0.9070 (m-80) REVERT: G 41 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8408 (tm-30) REVERT: G 62 ILE cc_start: 0.9578 (mm) cc_final: 0.9322 (tt) REVERT: G 90 ASP cc_start: 0.8368 (t70) cc_final: 0.7721 (t0) REVERT: H 31 LYS cc_start: 0.9304 (tppt) cc_final: 0.9086 (mptp) REVERT: H 65 ASP cc_start: 0.9503 (t0) cc_final: 0.9216 (t0) REVERT: H 80 TYR cc_start: 0.9209 (m-10) cc_final: 0.8684 (m-10) REVERT: H 102 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8685 (mm-30) REVERT: K 27 ASP cc_start: 0.9224 (t0) cc_final: 0.8943 (t0) REVERT: K 69 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9263 (pp) REVERT: K 72 ASP cc_start: 0.9001 (t0) cc_final: 0.8752 (t0) REVERT: K 86 LEU cc_start: 0.9180 (tm) cc_final: 0.8979 (pt) REVERT: L 23 GLU cc_start: 0.9388 (mt-10) cc_final: 0.9077 (pt0) REVERT: L 48 GLU cc_start: 0.9122 (mp0) cc_final: 0.8850 (pm20) REVERT: L 65 LYS cc_start: 0.8645 (mttt) cc_final: 0.8294 (mttm) REVERT: L 70 ARG cc_start: 0.9433 (mmt-90) cc_final: 0.9100 (mmt-90) REVERT: L 86 GLU cc_start: 0.9032 (pt0) cc_final: 0.8811 (pp20) REVERT: L 101 ARG cc_start: 0.8724 (mmt-90) cc_final: 0.7450 (mmt180) REVERT: L 103 ASP cc_start: 0.8903 (t0) cc_final: 0.8254 (t0) REVERT: L 107 ASP cc_start: 0.9419 (m-30) cc_final: 0.8972 (m-30) outliers start: 26 outliers final: 15 residues processed: 258 average time/residue: 1.3575 time to fit residues: 378.6629 Evaluate side-chains 242 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 225 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 84 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 75 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.049456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.034589 restraints weight = 60242.807| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 2.24 r_work: 0.2487 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14172 Z= 0.195 Angle : 0.592 9.724 20397 Z= 0.341 Chirality : 0.036 0.184 2350 Planarity : 0.004 0.038 1587 Dihedral : 29.586 124.225 4181 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.71 % Allowed : 27.53 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.27), residues: 939 helix: 2.49 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.12 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE D 62 TYR 0.013 0.001 TYR D 34 ARG 0.008 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 835) hydrogen bonds : angle 2.92361 ( 2097) metal coordination : bond 0.01370 ( 16) metal coordination : angle 2.06035 ( 18) covalent geometry : bond 0.00440 (14156) covalent geometry : angle 0.58898 (20379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8175 (pm20) cc_final: 0.7907 (pm20) REVERT: A 76 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8925 (tt0) REVERT: A 129 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8839 (tpt90) REVERT: C 59 THR cc_start: 0.9589 (m) cc_final: 0.9369 (t) REVERT: C 72 ASP cc_start: 0.9413 (t0) cc_final: 0.9157 (m-30) REVERT: C 73 ASN cc_start: 0.9424 (t0) cc_final: 0.8786 (t0) REVERT: C 91 GLU cc_start: 0.9271 (tt0) cc_final: 0.8707 (tp30) REVERT: C 104 GLN cc_start: 0.8974 (mm110) cc_final: 0.8556 (mm110) REVERT: C 116 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8294 (mm) REVERT: D 39 TYR cc_start: 0.8826 (t80) cc_final: 0.8588 (t80) REVERT: D 42 LEU cc_start: 0.9415 (tp) cc_final: 0.9153 (tp) REVERT: D 65 ASP cc_start: 0.9401 (t0) cc_final: 0.9093 (OUTLIER) REVERT: D 102 GLU cc_start: 0.9249 (tp30) cc_final: 0.8555 (tp30) REVERT: D 112 THR cc_start: 0.9638 (m) cc_final: 0.9339 (p) REVERT: E 59 GLU cc_start: 0.8958 (pm20) cc_final: 0.8510 (pm20) REVERT: E 73 GLU cc_start: 0.9034 (tt0) cc_final: 0.8730 (tt0) REVERT: E 94 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8728 (mm-30) REVERT: F 88 TYR cc_start: 0.9319 (m-10) cc_final: 0.9111 (m-80) REVERT: F 92 ARG cc_start: 0.9446 (OUTLIER) cc_final: 0.8972 (mmm-85) REVERT: G 41 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8428 (tm-30) REVERT: G 62 ILE cc_start: 0.9578 (mm) cc_final: 0.9339 (tt) REVERT: G 90 ASP cc_start: 0.8409 (t70) cc_final: 0.7762 (t0) REVERT: H 31 LYS cc_start: 0.9293 (tppt) cc_final: 0.9024 (mptp) REVERT: H 65 ASP cc_start: 0.9524 (t0) cc_final: 0.9202 (t0) REVERT: H 80 TYR cc_start: 0.9193 (m-10) cc_final: 0.8740 (m-10) REVERT: K 27 ASP cc_start: 0.9204 (t0) cc_final: 0.8888 (t0) REVERT: K 69 ILE cc_start: 0.9530 (OUTLIER) cc_final: 0.9263 (pp) REVERT: K 72 ASP cc_start: 0.9046 (t0) cc_final: 0.8728 (t0) REVERT: K 91 MET cc_start: 0.9064 (mmm) cc_final: 0.8811 (tpp) REVERT: L 48 GLU cc_start: 0.9182 (mp0) cc_final: 0.8902 (pm20) REVERT: L 65 LYS cc_start: 0.8834 (mttt) cc_final: 0.8139 (mttm) REVERT: L 70 ARG cc_start: 0.9402 (mmt-90) cc_final: 0.9194 (mmt-90) REVERT: L 101 ARG cc_start: 0.8739 (mmt-90) cc_final: 0.7609 (mmt-90) REVERT: L 103 ASP cc_start: 0.8839 (t0) cc_final: 0.8243 (t0) REVERT: L 107 ASP cc_start: 0.9413 (m-30) cc_final: 0.8967 (m-30) outliers start: 29 outliers final: 23 residues processed: 251 average time/residue: 1.4055 time to fit residues: 380.2409 Evaluate side-chains 245 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.0170 chunk 93 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- 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** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.050315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.035663 restraints weight = 60960.743| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.26 r_work: 0.2521 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14172 Z= 0.148 Angle : 0.590 11.168 20397 Z= 0.338 Chirality : 0.035 0.206 2350 Planarity : 0.004 0.034 1587 Dihedral : 29.387 122.923 4181 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 30.09 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.27), residues: 939 helix: 2.56 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.09 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP L 17 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE D 67 TYR 0.013 0.001 TYR D 34 ARG 0.008 0.000 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03150 ( 835) hydrogen bonds : angle 2.86078 ( 2097) metal coordination : bond 0.00474 ( 16) metal coordination : angle 2.00526 ( 18) covalent geometry : bond 0.00328 (14156) covalent geometry : angle 0.58695 (20379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8901 (tt0) REVERT: A 122 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8793 (pttp) REVERT: C 59 THR cc_start: 0.9550 (m) cc_final: 0.9248 (t) REVERT: C 73 ASN cc_start: 0.9395 (t0) cc_final: 0.8830 (t0) REVERT: C 91 GLU cc_start: 0.9203 (tt0) cc_final: 0.8621 (tp30) REVERT: C 104 GLN cc_start: 0.8857 (mm110) cc_final: 0.8410 (mm110) REVERT: D 42 LEU cc_start: 0.9364 (tp) cc_final: 0.9109 (tp) REVERT: D 65 ASP cc_start: 0.9375 (t0) cc_final: 0.9057 (OUTLIER) REVERT: D 102 GLU cc_start: 0.9192 (tp30) cc_final: 0.8645 (tp30) REVERT: D 112 THR cc_start: 0.9588 (m) cc_final: 0.9319 (p) REVERT: E 59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8368 (pm20) REVERT: E 73 GLU cc_start: 0.9012 (tt0) cc_final: 0.8706 (tt0) REVERT: E 94 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8730 (mm-30) REVERT: F 92 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.8891 (mmm-85) REVERT: G 38 ASN cc_start: 0.8726 (m-40) cc_final: 0.8236 (p0) REVERT: G 41 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8284 (tm-30) REVERT: G 62 ILE cc_start: 0.9487 (mm) cc_final: 0.9248 (tt) REVERT: H 65 ASP cc_start: 0.9494 (t0) cc_final: 0.9178 (t0) REVERT: H 80 TYR cc_start: 0.9154 (m-10) cc_final: 0.8776 (m-10) REVERT: K 27 ASP cc_start: 0.9208 (t0) cc_final: 0.8887 (t0) REVERT: K 69 ILE cc_start: 0.9492 (pp) cc_final: 0.9244 (pp) REVERT: K 72 ASP cc_start: 0.9078 (t0) cc_final: 0.8704 (t0) REVERT: K 91 MET cc_start: 0.9201 (mmm) cc_final: 0.8868 (OUTLIER) REVERT: L 41 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8720 (p) REVERT: L 48 GLU cc_start: 0.9176 (mp0) cc_final: 0.8825 (pm20) REVERT: L 65 LYS cc_start: 0.8757 (mttt) cc_final: 0.8306 (mttm) REVERT: L 86 GLU cc_start: 0.8121 (pp20) cc_final: 0.7827 (pp20) REVERT: L 91 ARG cc_start: 0.9000 (tpp-160) cc_final: 0.8781 (tpp-160) REVERT: L 101 ARG cc_start: 0.8777 (mmt-90) cc_final: 0.7998 (mmt-90) REVERT: L 103 ASP cc_start: 0.8884 (t0) cc_final: 0.8262 (t0) REVERT: L 107 ASP cc_start: 0.9418 (m-30) cc_final: 0.8966 (m-30) outliers start: 26 outliers final: 17 residues processed: 252 average time/residue: 1.4210 time to fit residues: 388.8899 Evaluate side-chains 240 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.050282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.035378 restraints weight = 61766.960| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.30 r_work: 0.2519 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14172 Z= 0.174 Angle : 0.601 11.618 20397 Z= 0.341 Chirality : 0.035 0.166 2350 Planarity : 0.004 0.036 1587 Dihedral : 29.451 122.820 4181 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.46 % Allowed : 30.99 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.27), residues: 939 helix: 2.58 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -0.01 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE K 97 TYR 0.027 0.001 TYR F 88 ARG 0.011 0.000 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.03268 ( 835) hydrogen bonds : angle 2.89443 ( 2097) metal coordination : bond 0.00995 ( 16) metal coordination : angle 1.94029 ( 18) covalent geometry : bond 0.00390 (14156) covalent geometry : angle 0.59828 (20379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8918 (tt0) REVERT: A 122 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8729 (pttp) REVERT: A 129 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8853 (tpt90) REVERT: C 72 ASP cc_start: 0.9378 (t0) cc_final: 0.9052 (m-30) REVERT: C 73 ASN cc_start: 0.9361 (t0) cc_final: 0.8727 (t0) REVERT: C 91 GLU cc_start: 0.9223 (tt0) cc_final: 0.8638 (tp30) REVERT: C 104 GLN cc_start: 0.8880 (mm110) cc_final: 0.8470 (mm110) REVERT: D 42 LEU cc_start: 0.9319 (tp) cc_final: 0.9067 (tp) REVERT: D 65 ASP cc_start: 0.9383 (t0) cc_final: 0.9052 (OUTLIER) REVERT: D 112 THR cc_start: 0.9572 (m) cc_final: 0.9294 (p) REVERT: E 59 GLU cc_start: 0.8828 (pm20) cc_final: 0.8331 (pm20) REVERT: E 73 GLU cc_start: 0.8997 (tt0) cc_final: 0.8773 (tt0) REVERT: F 88 TYR cc_start: 0.9275 (m-80) cc_final: 0.8952 (m-80) REVERT: F 92 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8847 (mmm-85) REVERT: G 38 ASN cc_start: 0.8802 (m-40) cc_final: 0.8332 (p0) REVERT: G 41 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8311 (tm-30) REVERT: G 62 ILE cc_start: 0.9477 (mm) cc_final: 0.9248 (tt) REVERT: G 90 ASP cc_start: 0.8313 (t0) cc_final: 0.7628 (t0) REVERT: H 31 LYS cc_start: 0.9228 (tppt) cc_final: 0.8997 (mptp) REVERT: H 65 ASP cc_start: 0.9531 (t0) cc_final: 0.9195 (t0) REVERT: H 73 GLU cc_start: 0.9369 (tp30) cc_final: 0.9167 (tp30) REVERT: H 80 TYR cc_start: 0.8981 (m-10) cc_final: 0.8609 (m-10) REVERT: K 27 ASP cc_start: 0.9255 (t0) cc_final: 0.8929 (t0) REVERT: K 69 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9214 (pp) REVERT: K 72 ASP cc_start: 0.9104 (t0) cc_final: 0.8683 (t0) REVERT: K 91 MET cc_start: 0.9230 (mmm) cc_final: 0.8902 (mmp) REVERT: L 103 ASP cc_start: 0.8875 (t0) cc_final: 0.8334 (t0) REVERT: L 106 PHE cc_start: 0.9533 (OUTLIER) cc_final: 0.9103 (t80) REVERT: L 107 ASP cc_start: 0.9420 (m-30) cc_final: 0.8985 (m-30) outliers start: 27 outliers final: 18 residues processed: 250 average time/residue: 1.4444 time to fit residues: 390.0047 Evaluate side-chains 243 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 35 ARG Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 84 ASN Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 112 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.050893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.036104 restraints weight = 61663.579| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 2.31 r_work: 0.2548 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14172 Z= 0.152 Angle : 0.619 12.579 20397 Z= 0.346 Chirality : 0.034 0.176 2350 Planarity : 0.004 0.035 1587 Dihedral : 29.325 122.330 4181 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.71 % Allowed : 31.37 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.27), residues: 939 helix: 2.54 (0.20), residues: 619 sheet: None (None), residues: 0 loop : 0.02 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE D 67 TYR 0.018 0.001 TYR F 88 ARG 0.011 0.001 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 835) hydrogen bonds : angle 2.87953 ( 2097) metal coordination : bond 0.00715 ( 16) metal coordination : angle 2.15232 ( 18) covalent geometry : bond 0.00340 (14156) covalent geometry : angle 0.61589 (20379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8901 (tt0) REVERT: A 122 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8694 (pttp) REVERT: A 129 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8860 (tpt90) REVERT: B 53 GLU cc_start: 0.9309 (tp30) cc_final: 0.9102 (mm-30) REVERT: C 73 ASN cc_start: 0.9350 (t0) cc_final: 0.8806 (t0) REVERT: C 91 GLU cc_start: 0.9194 (tt0) cc_final: 0.8623 (tp30) REVERT: C 104 GLN cc_start: 0.8866 (mm110) cc_final: 0.8399 (mm110) REVERT: C 116 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8143 (mm) REVERT: D 42 LEU cc_start: 0.9282 (tp) cc_final: 0.9022 (tp) REVERT: D 65 ASP cc_start: 0.9370 (t0) cc_final: 0.9037 (OUTLIER) REVERT: D 112 THR cc_start: 0.9551 (m) cc_final: 0.9279 (p) REVERT: E 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8271 (pm20) REVERT: E 73 GLU cc_start: 0.8965 (tt0) cc_final: 0.8749 (tt0) REVERT: E 94 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8652 (mm-30) REVERT: F 87 VAL cc_start: 0.9490 (p) cc_final: 0.9276 (m) REVERT: F 88 TYR cc_start: 0.9245 (m-80) cc_final: 0.8970 (m-80) REVERT: G 38 ASN cc_start: 0.8804 (m-40) cc_final: 0.8440 (p0) REVERT: G 41 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8208 (tm-30) REVERT: G 62 ILE cc_start: 0.9434 (mm) cc_final: 0.9200 (tt) REVERT: H 31 LYS cc_start: 0.9206 (tppt) cc_final: 0.8873 (mptp) REVERT: H 65 ASP cc_start: 0.9495 (t0) cc_final: 0.9163 (t0) REVERT: H 80 TYR cc_start: 0.8995 (m-10) cc_final: 0.8603 (m-10) REVERT: K 27 ASP cc_start: 0.9271 (t0) cc_final: 0.8941 (t0) REVERT: K 69 ILE cc_start: 0.9486 (OUTLIER) cc_final: 0.9217 (pp) REVERT: K 72 ASP cc_start: 0.9041 (t0) cc_final: 0.8550 (t0) REVERT: K 81 LYS cc_start: 0.9568 (mmtp) cc_final: 0.9171 (mmpt) REVERT: K 91 MET cc_start: 0.9207 (mmm) cc_final: 0.8880 (mmp) REVERT: L 48 GLU cc_start: 0.8984 (pm20) cc_final: 0.8618 (pm20) REVERT: L 86 GLU cc_start: 0.7874 (pp20) cc_final: 0.7627 (pp20) REVERT: L 97 LYS cc_start: 0.9176 (ptmm) cc_final: 0.8891 (pttp) REVERT: L 101 ARG cc_start: 0.8961 (mmt90) cc_final: 0.8746 (mmt90) REVERT: L 103 ASP cc_start: 0.8839 (t0) cc_final: 0.8177 (t0) REVERT: L 107 ASP cc_start: 0.9410 (m-30) cc_final: 0.8914 (m-30) outliers start: 29 outliers final: 17 residues processed: 258 average time/residue: 1.9394 time to fit residues: 541.0362 Evaluate side-chains 247 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 227 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033715 restraints weight = 61107.431| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 2.14 r_work: 0.2484 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 14172 Z= 0.299 Angle : 0.692 12.981 20397 Z= 0.385 Chirality : 0.040 0.199 2350 Planarity : 0.005 0.044 1587 Dihedral : 29.988 123.852 4181 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.59 % Allowed : 32.65 % Favored : 63.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.27), residues: 939 helix: 2.54 (0.21), residues: 613 sheet: None (None), residues: 0 loop : 0.02 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.007 0.001 PHE F 61 TYR 0.021 0.002 TYR B 88 ARG 0.012 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 835) hydrogen bonds : angle 3.13985 ( 2097) metal coordination : bond 0.02530 ( 16) metal coordination : angle 2.66165 ( 18) covalent geometry : bond 0.00675 (14156) covalent geometry : angle 0.68799 (20379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 226 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.9229 (tt0) cc_final: 0.8741 (tp30) REVERT: C 104 GLN cc_start: 0.9036 (mm110) cc_final: 0.8639 (mm110) REVERT: C 116 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8536 (mm) REVERT: D 42 LEU cc_start: 0.9465 (tp) cc_final: 0.9193 (tp) REVERT: D 65 ASP cc_start: 0.9400 (t0) cc_final: 0.9092 (OUTLIER) REVERT: E 59 GLU cc_start: 0.8934 (pm20) cc_final: 0.8442 (pm20) REVERT: E 73 GLU cc_start: 0.9052 (tt0) cc_final: 0.8838 (tt0) REVERT: E 94 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8590 (mm-30) REVERT: F 88 TYR cc_start: 0.9338 (m-10) cc_final: 0.9030 (m-80) REVERT: G 38 ASN cc_start: 0.8901 (m-40) cc_final: 0.8314 (p0) REVERT: G 41 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8378 (tm-30) REVERT: G 62 ILE cc_start: 0.9626 (mm) cc_final: 0.9420 (tt) REVERT: G 90 ASP cc_start: 0.8789 (t0) cc_final: 0.8182 (t0) REVERT: H 65 ASP cc_start: 0.9514 (t0) cc_final: 0.9147 (t0) REVERT: H 73 GLU cc_start: 0.9272 (tp30) cc_final: 0.9041 (mm-30) REVERT: H 80 TYR cc_start: 0.9156 (m-10) cc_final: 0.8754 (m-10) REVERT: H 102 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8434 (tm-30) REVERT: K 27 ASP cc_start: 0.9155 (t0) cc_final: 0.8848 (t0) REVERT: K 69 ILE cc_start: 0.9551 (OUTLIER) cc_final: 0.9277 (pp) REVERT: K 72 ASP cc_start: 0.9120 (t0) cc_final: 0.8807 (t0) REVERT: K 81 LYS cc_start: 0.9637 (mmtp) cc_final: 0.9236 (mmpt) REVERT: K 91 MET cc_start: 0.9141 (mmm) cc_final: 0.8855 (mmp) REVERT: L 48 GLU cc_start: 0.8968 (pm20) cc_final: 0.8666 (pm20) REVERT: L 86 GLU cc_start: 0.7977 (pp20) cc_final: 0.7582 (pp20) REVERT: L 91 ARG cc_start: 0.9059 (tpp-160) cc_final: 0.8425 (mmp80) REVERT: L 103 ASP cc_start: 0.8881 (t0) cc_final: 0.8202 (t0) REVERT: L 106 PHE cc_start: 0.9443 (OUTLIER) cc_final: 0.8945 (t80) REVERT: L 107 ASP cc_start: 0.9302 (m-30) cc_final: 0.8806 (m-30) outliers start: 28 outliers final: 20 residues processed: 241 average time/residue: 1.3456 time to fit residues: 350.5364 Evaluate side-chains 236 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 66 GLU Chi-restraints excluded: chain L residue 106 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 15 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.049876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035111 restraints weight = 61020.735| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.31 r_work: 0.2505 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14172 Z= 0.171 Angle : 0.655 12.924 20397 Z= 0.363 Chirality : 0.036 0.193 2350 Planarity : 0.004 0.043 1587 Dihedral : 29.540 121.919 4181 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.69 % Allowed : 35.21 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.27), residues: 939 helix: 2.50 (0.20), residues: 613 sheet: None (None), residues: 0 loop : 0.05 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.016 0.001 TYR B 88 ARG 0.011 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.03319 ( 835) hydrogen bonds : angle 2.95875 ( 2097) metal coordination : bond 0.00855 ( 16) metal coordination : angle 2.66866 ( 18) covalent geometry : bond 0.00388 (14156) covalent geometry : angle 0.65030 (20379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8854 (tt0) REVERT: B 53 GLU cc_start: 0.9336 (tp30) cc_final: 0.9133 (mm-30) REVERT: C 73 ASN cc_start: 0.9314 (t0) cc_final: 0.8760 (t0) REVERT: C 91 GLU cc_start: 0.9193 (tt0) cc_final: 0.8658 (tp30) REVERT: C 104 GLN cc_start: 0.8912 (mm110) cc_final: 0.8472 (mm110) REVERT: C 116 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8380 (mm) REVERT: D 42 LEU cc_start: 0.9322 (tp) cc_final: 0.9065 (tp) REVERT: D 65 ASP cc_start: 0.9406 (t0) cc_final: 0.9161 (t0) REVERT: D 102 GLU cc_start: 0.9173 (tp30) cc_final: 0.8583 (tp30) REVERT: E 59 GLU cc_start: 0.8824 (pm20) cc_final: 0.8304 (pm20) REVERT: E 94 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8669 (mm-30) REVERT: F 88 TYR cc_start: 0.9252 (m-10) cc_final: 0.8988 (m-80) REVERT: F 93 GLN cc_start: 0.8849 (mt0) cc_final: 0.8641 (mp10) REVERT: G 38 ASN cc_start: 0.8824 (m-40) cc_final: 0.8408 (p0) REVERT: G 41 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8270 (tm-30) REVERT: G 62 ILE cc_start: 0.9466 (mm) cc_final: 0.9228 (tt) REVERT: G 90 ASP cc_start: 0.8450 (t0) cc_final: 0.7763 (t0) REVERT: H 31 LYS cc_start: 0.8004 (mptp) cc_final: 0.7803 (mmtt) REVERT: H 65 ASP cc_start: 0.9548 (t0) cc_final: 0.9174 (t0) REVERT: H 73 GLU cc_start: 0.9290 (tp30) cc_final: 0.9064 (mm-30) REVERT: H 80 TYR cc_start: 0.9086 (m-10) cc_final: 0.8704 (m-10) REVERT: H 102 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8191 (tm-30) REVERT: K 27 ASP cc_start: 0.9294 (t0) cc_final: 0.9046 (p0) REVERT: K 69 ILE cc_start: 0.9511 (OUTLIER) cc_final: 0.9252 (pp) REVERT: K 72 ASP cc_start: 0.9129 (t0) cc_final: 0.8688 (t0) REVERT: K 81 LYS cc_start: 0.9568 (mmtp) cc_final: 0.9175 (mmpt) REVERT: K 91 MET cc_start: 0.9191 (mmm) cc_final: 0.8810 (tpp) REVERT: L 48 GLU cc_start: 0.8929 (pm20) cc_final: 0.8618 (pm20) REVERT: L 65 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8466 (mmtp) REVERT: L 101 ARG cc_start: 0.9047 (mmt90) cc_final: 0.8451 (mmt-90) REVERT: L 103 ASP cc_start: 0.8932 (t0) cc_final: 0.8020 (t0) REVERT: L 107 ASP cc_start: 0.9355 (m-30) cc_final: 0.8962 (m-30) outliers start: 21 outliers final: 13 residues processed: 248 average time/residue: 1.3594 time to fit residues: 364.1632 Evaluate side-chains 243 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 227 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 65 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 73 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.050635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.035832 restraints weight = 61309.696| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.31 r_work: 0.2532 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14172 Z= 0.164 Angle : 0.669 13.402 20397 Z= 0.366 Chirality : 0.035 0.184 2350 Planarity : 0.005 0.050 1587 Dihedral : 29.463 122.058 4181 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.92 % Allowed : 36.49 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.27), residues: 939 helix: 2.55 (0.20), residues: 610 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP L 17 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.018 0.001 TYR B 88 ARG 0.011 0.001 ARG D 76 Details of bonding type rmsd hydrogen bonds : bond 0.03278 ( 835) hydrogen bonds : angle 2.93615 ( 2097) metal coordination : bond 0.00913 ( 16) metal coordination : angle 2.43970 ( 18) covalent geometry : bond 0.00371 (14156) covalent geometry : angle 0.66549 (20379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1878 Ramachandran restraints generated. 939 Oldfield, 0 Emsley, 939 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8750 (tt0) REVERT: C 56 GLU cc_start: 0.9042 (tt0) cc_final: 0.8493 (tt0) REVERT: C 73 ASN cc_start: 0.9293 (t0) cc_final: 0.8726 (t0) REVERT: C 91 GLU cc_start: 0.9183 (tt0) cc_final: 0.8609 (tp30) REVERT: C 104 GLN cc_start: 0.8894 (mm110) cc_final: 0.8425 (mm110) REVERT: C 116 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8301 (mm) REVERT: D 42 LEU cc_start: 0.9319 (tp) cc_final: 0.9069 (tp) REVERT: D 65 ASP cc_start: 0.9376 (t0) cc_final: 0.9158 (t0) REVERT: D 102 GLU cc_start: 0.9099 (tp30) cc_final: 0.8506 (tp30) REVERT: E 59 GLU cc_start: 0.8795 (pm20) cc_final: 0.8299 (pm20) REVERT: E 73 GLU cc_start: 0.8963 (tt0) cc_final: 0.8413 (tt0) REVERT: E 94 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8663 (mm-30) REVERT: F 87 VAL cc_start: 0.9520 (p) cc_final: 0.9319 (m) REVERT: F 88 TYR cc_start: 0.9261 (m-10) cc_final: 0.9000 (m-80) REVERT: G 38 ASN cc_start: 0.8893 (m-40) cc_final: 0.8616 (p0) REVERT: G 41 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8205 (tm-30) REVERT: G 62 ILE cc_start: 0.9452 (mm) cc_final: 0.9206 (tt) REVERT: H 65 ASP cc_start: 0.9514 (t0) cc_final: 0.9176 (t0) REVERT: H 73 GLU cc_start: 0.9312 (tp30) cc_final: 0.9058 (mm-30) REVERT: H 80 TYR cc_start: 0.9073 (m-10) cc_final: 0.8689 (m-10) REVERT: H 102 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8201 (tm-30) REVERT: K 27 ASP cc_start: 0.9273 (t0) cc_final: 0.8893 (t0) REVERT: K 69 ILE cc_start: 0.9513 (OUTLIER) cc_final: 0.9249 (pp) REVERT: K 72 ASP cc_start: 0.9121 (t0) cc_final: 0.8835 (t0) REVERT: K 91 MET cc_start: 0.9198 (mmm) cc_final: 0.8786 (tpp) REVERT: L 61 THR cc_start: 0.9655 (m) cc_final: 0.9117 (p) REVERT: L 86 GLU cc_start: 0.7983 (pp20) cc_final: 0.7186 (pp20) REVERT: L 91 ARG cc_start: 0.8960 (tpp-160) cc_final: 0.8137 (mmp80) REVERT: L 101 ARG cc_start: 0.9107 (mmt90) cc_final: 0.8591 (mmt-90) REVERT: L 103 ASP cc_start: 0.8903 (t0) cc_final: 0.7761 (t0) REVERT: L 107 ASP cc_start: 0.9284 (m-30) cc_final: 0.8675 (m-30) outliers start: 15 outliers final: 11 residues processed: 237 average time/residue: 1.3525 time to fit residues: 346.5671 Evaluate side-chains 241 residues out of total 820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain K residue 42 CYS Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.050873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.036050 restraints weight = 61455.805| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.30 r_work: 0.2544 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14172 Z= 0.160 Angle : 0.663 13.191 20397 Z= 0.364 Chirality : 0.035 0.192 2350 Planarity : 0.005 0.051 1587 Dihedral : 29.420 122.268 4181 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.05 % Allowed : 36.62 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.27), residues: 939 helix: 2.53 (0.20), residues: 610 sheet: None (None), residues: 0 loop : 0.01 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP L 17 HIS 0.005 0.001 HIS B 75 PHE 0.009 0.001 PHE D 67 TYR 0.015 0.001 TYR B 88 ARG 0.012 0.001 ARG L 70 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 835) hydrogen bonds : angle 2.92059 ( 2097) metal coordination : bond 0.00924 ( 16) metal coordination : angle 2.53506 ( 18) covalent geometry : bond 0.00362 (14156) covalent geometry : angle 0.65887 (20379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10223.18 seconds wall clock time: 178 minutes 28.62 seconds (10708.62 seconds total)