Starting phenix.real_space_refine on Sun May 25 03:45:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.map" model { file = "/net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rup_19513/05_2025/8rup_19513.cif" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1807 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 294 5.49 5 S 25 5.16 5 C 7915 2.51 5 N 2603 2.21 5 O 3184 1.98 5 H 11444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 25466 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1634 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1676 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1472 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1723 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1691 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1444 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4679 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4643 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2031 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 9, 'TRANS': 126} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "L" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1264 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 602 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22345 SG CYS K 57 71.571 122.968 49.361 1.00 50.10 S ATOM 22395 SG CYS K 60 68.788 120.963 50.604 1.00 60.04 S ATOM 22747 SG CYS K 84 68.939 124.690 51.631 1.00 59.08 S Time building chain proxies: 12.55, per 1000 atoms: 0.49 Number of scatterers: 25466 At special positions: 0 Unit cell: (103.75, 155.21, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 25 16.00 P 294 15.00 O 3184 8.00 N 2603 7.00 C 7915 6.00 H 11444 1.00 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: 6.20 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" NE2 HIS K 77 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 60 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 57 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 84 " Number of angles added : 3 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 72.3% alpha, 3.0% beta 147 base pairs and 271 stacking pairs defined. Time for finding SS restraints: 12.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.560A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.628A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.539A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 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 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.777A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.663A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.582A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.876A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.490A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.730A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 13 Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 34 through 41 Processing helix chain 'K' and resid 72 through 81 Processing helix chain 'K' and resid 84 through 89 Processing helix chain 'K' and resid 92 through 96 removed outlier: 3.952A pdb=" N LEU K 96 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 139 Processing helix chain 'L' and resid 9 through 60 removed outlier: 3.529A pdb=" N ASP L 29 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU L 33 " --> pdb=" O ASP L 29 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE L 34 " --> pdb=" O ARG L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 67 Processing helix chain 'L' and resid 69 through 75 removed outlier: 3.572A pdb=" N TYR L 73 " --> pdb=" O ASN L 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 45 removed outlier: 4.171A pdb=" N GLU M 13 " --> pdb=" O ILE M 9 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.132A 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 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.220A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AA8, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.840A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.197A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 550 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 271 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11433 1.02 - 1.22: 81 1.22 - 1.42: 6732 1.42 - 1.62: 8035 1.62 - 1.82: 40 Bond restraints: 26321 Sorted by residual: bond pdb=" CG2 TPO E 3 " pdb="HG23 TPO E 3 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN K 50 " pdb="HD22 ASN K 50 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CB TPO E 3 " pdb=" HB TPO E 3 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" CG2 TPO E 3 " pdb="HG21 TPO E 3 " ideal model delta sigma weight residual 0.970 1.090 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN K 50 " pdb="HD21 ASN K 50 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 26316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 47527 2.79 - 5.58: 136 5.58 - 8.37: 9 8.37 - 11.15: 2 11.15 - 13.94: 1 Bond angle restraints: 47675 Sorted by residual: angle pdb=" N VAL L 32 " pdb=" CA VAL L 32 " pdb=" C VAL L 32 " ideal model delta sigma weight residual 110.36 114.37 -4.01 1.05e+00 9.07e-01 1.46e+01 angle pdb=" N LEU H 101 " pdb=" CA LEU H 101 " pdb=" C LEU H 101 " ideal model delta sigma weight residual 111.56 117.26 -5.70 1.53e+00 4.27e-01 1.39e+01 angle pdb=" N ILE K 19 " pdb=" CA ILE K 19 " pdb=" C ILE K 19 " ideal model delta sigma weight residual 112.35 107.34 5.01 1.41e+00 5.03e-01 1.26e+01 angle pdb=" N ARG K 106 " pdb=" CA ARG K 106 " pdb=" C ARG K 106 " ideal model delta sigma weight residual 110.97 107.30 3.67 1.09e+00 8.42e-01 1.13e+01 angle pdb=" CB LYS M 18 " pdb=" CG LYS M 18 " pdb=" CD LYS M 18 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 ... (remaining 47670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 9337 33.26 - 66.51: 1794 66.51 - 99.77: 26 99.77 - 133.03: 0 133.03 - 166.28: 1 Dihedral angle restraints: 11158 sinusoidal: 7790 harmonic: 3368 Sorted by residual: dihedral pdb=" C4' DG I 36 " pdb=" C3' DG I 36 " pdb=" O3' DG I 36 " pdb=" P DG I 37 " ideal model delta sinusoidal sigma weight residual 220.00 53.72 166.28 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA GLU K 63 " pdb=" C GLU K 63 " pdb=" N LEU K 64 " pdb=" CA LEU K 64 " ideal model delta harmonic sigma weight residual 180.00 -162.94 -17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.28 -16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 11155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1759 0.045 - 0.090: 570 0.090 - 0.135: 101 0.135 - 0.180: 4 0.180 - 0.226: 1 Chirality restraints: 2435 Sorted by residual: chirality pdb=" C3' DG I 36 " pdb=" C4' DG I 36 " pdb=" O3' DG I 36 " pdb=" C2' DG I 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA LEU H 101 " pdb=" N LEU H 101 " pdb=" C LEU H 101 " pdb=" CB LEU H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.92e-01 chirality pdb=" CA ILE B 46 " pdb=" N ILE B 46 " pdb=" C ILE B 46 " pdb=" CB ILE B 46 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2432 not shown) Planarity restraints: 2898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN K 50 " 0.298 2.00e-02 2.50e+03 3.30e-01 1.64e+03 pdb=" CG ASN K 50 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN K 50 " -0.286 2.00e-02 2.50e+03 pdb=" ND2 ASN K 50 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN K 50 " -0.484 2.00e-02 2.50e+03 pdb="HD22 ASN K 50 " 0.500 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 75 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" CD GLU K 75 " -0.063 2.00e-02 2.50e+03 pdb=" OE1 GLU K 75 " 0.022 2.00e-02 2.50e+03 pdb=" OE2 GLU K 75 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU L 25 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.78e+00 pdb=" C LEU L 25 " -0.045 2.00e-02 2.50e+03 pdb=" O LEU L 25 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS L 26 " 0.015 2.00e-02 2.50e+03 ... (remaining 2895 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1697 2.21 - 2.81: 45394 2.81 - 3.40: 64234 3.40 - 4.00: 93487 4.00 - 4.60: 138882 Nonbonded interactions: 343694 Sorted by model distance: nonbonded pdb=" OE1 GLU A 59 " pdb=" H GLU A 59 " model vdw 1.610 2.450 nonbonded pdb=" H GLU K 68 " pdb=" OD2 ASP K 71 " model vdw 1.611 2.450 nonbonded pdb=" OE2 GLU B 52 " pdb="HH11 ARG B 55 " model vdw 1.620 2.450 nonbonded pdb=" OE1 GLN K 92 " pdb=" H PHE K 93 " model vdw 1.647 2.450 nonbonded pdb=" OE1 GLU E 59 " pdb=" H GLU E 59 " model vdw 1.663 2.450 ... (remaining 343689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 37 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 38 through 76 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 78 through 80 or (resid \ 81 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 82 through 134)) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 118)) selection = (chain 'G' and (resid 11 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 90 or (resid \ 91 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 92 through 118)) } ncs_group { reference = (chain 'D' and (resid 31 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 52 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 58 through 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 72 through 125)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.380 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 70.100 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.080 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 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 : 0.006 0.102 14881 Z= 0.263 Angle : 0.691 9.023 21378 Z= 0.414 Chirality : 0.043 0.226 2435 Planarity : 0.006 0.051 1696 Dihedral : 27.438 166.284 6260 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.73 % Allowed : 24.72 % Favored : 74.54 % 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: 1.21 (0.25), residues: 994 helix: 1.61 (0.19), residues: 701 sheet: None (None), residues: 0 loop : -1.16 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP K 25 HIS 0.010 0.002 HIS K 17 PHE 0.016 0.002 PHE M 22 TYR 0.025 0.002 TYR L 73 ARG 0.017 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.11491 ( 926) hydrogen bonds : angle 4.09814 ( 2354) metal coordination : bond 0.00702 ( 4) metal coordination : angle 4.66709 ( 3) covalent geometry : bond 0.00567 (14877) covalent geometry : angle 0.68886 (21375) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 277 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7215 (mm-40) REVERT: D 35 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6717 (mt-10) REVERT: G 36 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8026 (mptm) REVERT: L 38 GLN cc_start: 0.7082 (tp40) cc_final: 0.6829 (tp40) REVERT: M 38 GLN cc_start: 0.7941 (tp40) cc_final: 0.7654 (tp-100) outliers start: 6 outliers final: 3 residues processed: 279 average time/residue: 3.6147 time to fit residues: 1074.3667 Evaluate side-chains 268 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 264 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 132 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 25 ASN B 64 ASN D 84 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.170498 restraints weight = 64521.437| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.11 r_work: 0.3673 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14881 Z= 0.244 Angle : 0.638 5.434 21378 Z= 0.385 Chirality : 0.042 0.137 2435 Planarity : 0.005 0.051 1696 Dihedral : 29.536 170.820 4344 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.69 % Allowed : 21.42 % Favored : 75.89 % 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: 1.49 (0.25), residues: 994 helix: 1.81 (0.19), residues: 717 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 70 HIS 0.008 0.002 HIS K 17 PHE 0.015 0.002 PHE M 22 TYR 0.025 0.002 TYR B 51 ARG 0.008 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.05275 ( 926) hydrogen bonds : angle 3.29902 ( 2354) metal coordination : bond 0.01312 ( 4) metal coordination : angle 1.47357 ( 3) covalent geometry : bond 0.00541 (14877) covalent geometry : angle 0.63807 (21375) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 271 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8274 (mtp85) cc_final: 0.8066 (mtp180) REVERT: B 92 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7669 (ttp80) REVERT: C 104 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7316 (mm-40) REVERT: G 36 LYS cc_start: 0.8345 (mptm) cc_final: 0.7982 (mptm) REVERT: L 38 GLN cc_start: 0.7329 (tp40) cc_final: 0.6798 (tp40) REVERT: M 33 TRP cc_start: 0.7744 (t60) cc_final: 0.7028 (t60) outliers start: 22 outliers final: 14 residues processed: 272 average time/residue: 3.6231 time to fit residues: 1048.7121 Evaluate side-chains 277 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 262 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 44 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 123 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 73 ASN D 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.169028 restraints weight = 64500.548| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.18 r_work: 0.3692 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14881 Z= 0.196 Angle : 0.605 6.991 21378 Z= 0.366 Chirality : 0.039 0.130 2435 Planarity : 0.005 0.061 1696 Dihedral : 29.444 168.975 4332 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.94 % Allowed : 22.03 % Favored : 75.03 % 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: 1.87 (0.26), residues: 994 helix: 2.11 (0.19), residues: 718 sheet: -2.67 (1.67), residues: 10 loop : -1.09 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 70 HIS 0.006 0.001 HIS K 17 PHE 0.015 0.001 PHE K 61 TYR 0.017 0.001 TYR B 51 ARG 0.009 0.001 ARG K 132 Details of bonding type rmsd hydrogen bonds : bond 0.04687 ( 926) hydrogen bonds : angle 3.18408 ( 2354) metal coordination : bond 0.00503 ( 4) metal coordination : angle 1.81542 ( 3) covalent geometry : bond 0.00431 (14877) covalent geometry : angle 0.60420 (21375) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 262 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: C 42 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7886 (mtp-110) REVERT: C 104 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7323 (mm-40) REVERT: G 36 LYS cc_start: 0.8314 (mptm) cc_final: 0.7978 (mptm) REVERT: L 38 GLN cc_start: 0.7347 (tp40) cc_final: 0.6762 (tp40) outliers start: 24 outliers final: 14 residues processed: 267 average time/residue: 3.7000 time to fit residues: 1055.3629 Evaluate side-chains 273 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 73 TYR Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 26 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.1980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 73 ASN D 84 ASN H 63 ASN ** K 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.167768 restraints weight = 62657.497| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.19 r_work: 0.3666 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14881 Z= 0.224 Angle : 0.612 4.731 21378 Z= 0.371 Chirality : 0.041 0.134 2435 Planarity : 0.005 0.080 1696 Dihedral : 29.426 170.423 4332 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.55 % Allowed : 21.05 % Favored : 75.40 % 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: 1.80 (0.26), residues: 994 helix: 2.05 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.14 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 70 HIS 0.007 0.001 HIS K 17 PHE 0.017 0.002 PHE K 22 TYR 0.017 0.002 TYR B 51 ARG 0.009 0.001 ARG K 132 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 926) hydrogen bonds : angle 3.19034 ( 2354) metal coordination : bond 0.00678 ( 4) metal coordination : angle 2.18097 ( 3) covalent geometry : bond 0.00495 (14877) covalent geometry : angle 0.61121 (21375) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 257 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: A 131 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7156 (mtp85) REVERT: C 104 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7316 (mm-40) REVERT: K 53 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.5523 (p0) REVERT: K 132 ARG cc_start: 0.7845 (ttt90) cc_final: 0.7393 (ttt90) REVERT: L 38 GLN cc_start: 0.7582 (tp40) cc_final: 0.7012 (tp40) REVERT: M 38 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8183 (tm-30) outliers start: 29 outliers final: 16 residues processed: 266 average time/residue: 3.5956 time to fit residues: 1018.2943 Evaluate side-chains 271 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 73 TYR Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN H 63 ASN K 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.167447 restraints weight = 63418.589| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.17 r_work: 0.3665 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14881 Z= 0.219 Angle : 0.607 6.131 21378 Z= 0.369 Chirality : 0.040 0.133 2435 Planarity : 0.005 0.065 1696 Dihedral : 29.427 169.554 4332 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.43 % Allowed : 21.91 % Favored : 74.66 % 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: 1.93 (0.26), residues: 994 helix: 2.12 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 70 HIS 0.007 0.001 HIS K 17 PHE 0.015 0.002 PHE K 22 TYR 0.014 0.002 TYR B 51 ARG 0.011 0.001 ARG G 20 Details of bonding type rmsd hydrogen bonds : bond 0.04786 ( 926) hydrogen bonds : angle 3.17681 ( 2354) metal coordination : bond 0.00613 ( 4) metal coordination : angle 2.60623 ( 3) covalent geometry : bond 0.00486 (14877) covalent geometry : angle 0.60675 (21375) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 255 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7153 (mtp85) REVERT: C 104 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7313 (mm-40) REVERT: G 36 LYS cc_start: 0.8349 (mptm) cc_final: 0.8000 (mptm) REVERT: K 53 ASP cc_start: 0.6395 (OUTLIER) cc_final: 0.5548 (p0) REVERT: M 38 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8164 (tm-30) outliers start: 28 outliers final: 19 residues processed: 264 average time/residue: 3.6623 time to fit residues: 1028.7359 Evaluate side-chains 273 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 39 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN D 84 ASN H 63 ASN M 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.167649 restraints weight = 63185.790| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.17 r_work: 0.3670 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14881 Z= 0.205 Angle : 0.606 6.729 21378 Z= 0.367 Chirality : 0.039 0.130 2435 Planarity : 0.006 0.086 1696 Dihedral : 29.415 169.641 4332 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 22.64 % Favored : 73.81 % 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: 2.00 (0.26), residues: 994 helix: 2.18 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 70 HIS 0.006 0.001 HIS K 17 PHE 0.015 0.002 PHE K 22 TYR 0.013 0.002 TYR B 51 ARG 0.011 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 926) hydrogen bonds : angle 3.13551 ( 2354) metal coordination : bond 0.00825 ( 4) metal coordination : angle 2.58960 ( 3) covalent geometry : bond 0.00453 (14877) covalent geometry : angle 0.60499 (21375) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: A 131 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7163 (mtp85) REVERT: C 104 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7306 (mm-40) REVERT: G 36 LYS cc_start: 0.8351 (mptm) cc_final: 0.8002 (mptm) REVERT: K 132 ARG cc_start: 0.7898 (ttt90) cc_final: 0.7610 (ttt90) REVERT: M 38 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8179 (tm-30) outliers start: 29 outliers final: 19 residues processed: 265 average time/residue: 3.7436 time to fit residues: 1055.1687 Evaluate side-chains 275 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.168059 restraints weight = 63367.409| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.17 r_work: 0.3674 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14881 Z= 0.185 Angle : 0.602 9.490 21378 Z= 0.364 Chirality : 0.038 0.142 2435 Planarity : 0.005 0.071 1696 Dihedral : 29.412 169.378 4332 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.67 % Allowed : 23.01 % Favored : 73.32 % 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: 2.14 (0.26), residues: 994 helix: 2.28 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 70 HIS 0.005 0.001 HIS K 17 PHE 0.014 0.001 PHE K 22 TYR 0.012 0.001 TYR B 51 ARG 0.012 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04453 ( 926) hydrogen bonds : angle 3.14342 ( 2354) metal coordination : bond 0.00642 ( 4) metal coordination : angle 2.11965 ( 3) covalent geometry : bond 0.00408 (14877) covalent geometry : angle 0.60168 (21375) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 288 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: A 131 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7154 (mtp85) REVERT: C 104 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7322 (mm-40) REVERT: G 36 LYS cc_start: 0.8359 (mptm) cc_final: 0.8003 (mptm) REVERT: K 24 ASN cc_start: 0.5630 (OUTLIER) cc_final: 0.5358 (p0) REVERT: M 38 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8185 (tm-30) outliers start: 30 outliers final: 22 residues processed: 266 average time/residue: 3.6280 time to fit residues: 1032.0167 Evaluate side-chains 276 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 73 ASN D 84 ASN ** M 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.183470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.168054 restraints weight = 62914.902| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.15 r_work: 0.3667 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14881 Z= 0.215 Angle : 0.620 8.630 21378 Z= 0.373 Chirality : 0.040 0.159 2435 Planarity : 0.006 0.072 1696 Dihedral : 29.400 169.593 4332 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.55 % Allowed : 23.99 % Favored : 72.46 % 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: 2.02 (0.26), residues: 994 helix: 2.19 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.02 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 70 HIS 0.005 0.001 HIS K 17 PHE 0.013 0.002 PHE K 93 TYR 0.012 0.002 TYR B 51 ARG 0.012 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 926) hydrogen bonds : angle 3.17456 ( 2354) metal coordination : bond 0.00688 ( 4) metal coordination : angle 2.40604 ( 3) covalent geometry : bond 0.00476 (14877) covalent geometry : angle 0.61921 (21375) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: A 131 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7137 (mtp85) REVERT: C 104 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7323 (mm-40) REVERT: G 36 LYS cc_start: 0.8343 (mptm) cc_final: 0.7988 (mptm) REVERT: M 38 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8159 (tm-30) outliers start: 29 outliers final: 21 residues processed: 262 average time/residue: 3.7560 time to fit residues: 1045.7529 Evaluate side-chains 274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 80 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN M 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.182648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.167404 restraints weight = 63154.555| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.16 r_work: 0.3659 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14881 Z= 0.240 Angle : 0.633 6.794 21378 Z= 0.380 Chirality : 0.042 0.143 2435 Planarity : 0.006 0.070 1696 Dihedral : 29.416 170.294 4332 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.79 % Allowed : 23.87 % Favored : 72.34 % 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: 1.87 (0.26), residues: 994 helix: 2.09 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.11 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 25 HIS 0.005 0.001 HIS K 17 PHE 0.015 0.002 PHE K 93 TYR 0.014 0.002 TYR B 51 ARG 0.013 0.001 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 926) hydrogen bonds : angle 3.25579 ( 2354) metal coordination : bond 0.00412 ( 4) metal coordination : angle 2.59171 ( 3) covalent geometry : bond 0.00534 (14877) covalent geometry : angle 0.63184 (21375) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 253 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (mt0) REVERT: A 131 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7155 (mtp85) REVERT: C 104 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7340 (mm-40) REVERT: G 36 LYS cc_start: 0.8323 (mptm) cc_final: 0.7968 (mptm) REVERT: L 33 GLU cc_start: 0.7189 (pm20) cc_final: 0.6931 (pm20) REVERT: M 38 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8167 (tm-30) outliers start: 31 outliers final: 25 residues processed: 264 average time/residue: 3.6630 time to fit residues: 1028.2772 Evaluate side-chains 279 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 HIS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.168887 restraints weight = 63411.751| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.17 r_work: 0.3674 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14881 Z= 0.176 Angle : 0.615 8.679 21378 Z= 0.370 Chirality : 0.038 0.158 2435 Planarity : 0.005 0.074 1696 Dihedral : 29.422 169.604 4332 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.43 % Allowed : 24.72 % Favored : 71.85 % 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: 2.12 (0.26), residues: 994 helix: 2.27 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP K 25 HIS 0.003 0.001 HIS K 17 PHE 0.014 0.001 PHE M 22 TYR 0.012 0.001 TYR B 51 ARG 0.015 0.001 ARG K 108 Details of bonding type rmsd hydrogen bonds : bond 0.04451 ( 926) hydrogen bonds : angle 3.16748 ( 2354) metal coordination : bond 0.00545 ( 4) metal coordination : angle 2.18237 ( 3) covalent geometry : bond 0.00387 (14877) covalent geometry : angle 0.61402 (21375) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1988 Ramachandran restraints generated. 994 Oldfield, 0 Emsley, 994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 4 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue LYS 129 is missing expected H atoms. Skipping. Residue LYS 130 is missing expected H atoms. Skipping. Residue ILE 135 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: A 131 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7176 (mtp85) REVERT: C 104 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7340 (mm-40) REVERT: G 36 LYS cc_start: 0.8337 (mptm) cc_final: 0.7978 (mptm) REVERT: M 38 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8152 (tm-30) outliers start: 28 outliers final: 23 residues processed: 259 average time/residue: 3.6686 time to fit residues: 1009.5914 Evaluate side-chains 274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain K residue 24 ASN Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 86 PHE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 93 PHE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 74 PHE Chi-restraints excluded: chain M residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.183884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.168506 restraints weight = 63569.594| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.17 r_work: 0.3684 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14881 Z= 0.169 Angle : 0.614 10.064 21378 Z= 0.369 Chirality : 0.037 0.165 2435 Planarity : 0.005 0.076 1696 Dihedral : 29.416 169.300 4332 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.06 % Allowed : 25.21 % Favored : 71.73 % 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: 2.19 (0.26), residues: 994 helix: 2.33 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -0.99 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K 25 HIS 0.004 0.001 HIS K 80 PHE 0.019 0.002 PHE M 22 TYR 0.011 0.001 TYR B 51 ARG 0.014 0.001 ARG K 108 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 926) hydrogen bonds : angle 3.15140 ( 2354) metal coordination : bond 0.00513 ( 4) metal coordination : angle 2.14099 ( 3) covalent geometry : bond 0.00371 (14877) covalent geometry : angle 0.61397 (21375) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24348.15 seconds wall clock time: 415 minutes 5.87 seconds (24905.87 seconds total)