Starting phenix.real_space_refine on Mon Aug 25 07:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rup_19513/08_2025/8rup_19513.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rup_19513/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rup_19513/08_2025/8rup_19513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rup_19513/08_2025/8rup_19513.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rup_19513/08_2025/8rup_19513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rup_19513/08_2025/8rup_19513.map" } resolution = 2.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ASP:plan': 2, 'ARG:plan': 1} 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: {'ASP:plan': 1, 'GLU: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: {'GLU:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 1} 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: {'ASP:plan': 1, 'ARG: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: 4.93, per 1000 atoms: 0.19 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: 2.37 Conformation dependent library (CDL) restraints added in 572.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 5.21 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: 6.59 Time building geometry restraints manager: 3.31 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.160 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 35.470 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.370 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.001 ARG G 20 TYR 0.025 0.002 TYR L 73 PHE 0.016 0.002 PHE M 22 TRP 0.025 0.004 TRP K 25 HIS 0.010 0.002 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00567 (14877) covalent geometry : angle 0.68886 (21375) hydrogen bonds : bond 0.11491 ( 926) hydrogen bonds : angle 4.09814 ( 2354) metal coordination : bond 0.00702 ( 4) metal coordination : angle 4.66709 ( 3) *********************** 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 : 0.591 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: 1.9856 time to fit residues: 586.8767 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 : 0.659 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 64 ASN F 25 ASN H 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.190093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.173938 restraints weight = 64957.150| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.25 r_work: 0.3708 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1230 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= 0.187 Angle : 0.606 5.854 21378 Z= 0.367 Chirality : 0.038 0.132 2435 Planarity : 0.005 0.047 1696 Dihedral : 29.517 170.356 4344 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.33 % Allowed : 21.54 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.26), residues: 994 helix: 2.07 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.018 0.001 TYR B 51 PHE 0.015 0.002 PHE M 22 TRP 0.011 0.002 TRP L 70 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00409 (14877) covalent geometry : angle 0.60554 (21375) hydrogen bonds : bond 0.04707 ( 926) hydrogen bonds : angle 3.21631 ( 2354) metal coordination : bond 0.01224 ( 4) metal coordination : angle 0.89288 ( 3) *********************** 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 285 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 266 time to evaluate : 0.627 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: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7639 (ttp80) REVERT: C 104 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7332 (mm-40) REVERT: L 38 GLN cc_start: 0.7129 (tp40) cc_final: 0.6717 (tp40) outliers start: 19 outliers final: 14 residues processed: 267 average time/residue: 2.0651 time to fit residues: 583.3880 Evaluate side-chains 274 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 132 ARG Chi-restraints excluded: chain L residue 8 SER 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 25 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 24 GLN C 73 ASN D 84 ASN H 49 HIS H 63 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.168430 restraints weight = 63402.584| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.22 r_work: 0.3658 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14881 Z= 0.247 Angle : 0.635 5.519 21378 Z= 0.384 Chirality : 0.042 0.142 2435 Planarity : 0.005 0.052 1696 Dihedral : 29.455 170.648 4336 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.16 % Allowed : 19.58 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.25), residues: 994 helix: 1.88 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -1.03 (0.31), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 20 TYR 0.025 0.002 TYR B 51 PHE 0.015 0.002 PHE M 22 TRP 0.018 0.003 TRP L 70 HIS 0.009 0.002 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00549 (14877) covalent geometry : angle 0.63444 (21375) hydrogen bonds : bond 0.05389 ( 926) hydrogen bonds : angle 3.30091 ( 2354) metal coordination : bond 0.00658 ( 4) metal coordination : angle 2.85845 ( 3) *********************** 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 298 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.593 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: 0.8328 (OUTLIER) cc_final: 0.8057 (mt0) REVERT: A 131 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7246 (mtp85) REVERT: C 42 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7861 (mtp-110) REVERT: C 104 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7322 (mm-40) REVERT: D 119 THR cc_start: 0.8525 (t) cc_final: 0.8324 (m) REVERT: K 53 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.5975 (p0) REVERT: L 38 GLN cc_start: 0.7488 (tp40) cc_final: 0.6878 (tp40) outliers start: 34 outliers final: 18 residues processed: 272 average time/residue: 1.9825 time to fit residues: 571.3766 Evaluate side-chains 275 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 53 GLU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain D residue 48 VAL 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 H residue 76 GLU 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 L residue 8 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 ILE 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 Chi-restraints excluded: chain M residue 37 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 64 ASN C 73 ASN D 84 ASN K 56 GLN 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 = 0.184508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.168966 restraints weight = 62751.659| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.21 r_work: 0.3671 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: 0.7121 moved from start: 0.2161 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= 0.206 Angle : 0.612 5.905 21378 Z= 0.371 Chirality : 0.040 0.134 2435 Planarity : 0.005 0.067 1696 Dihedral : 29.451 170.130 4332 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.92 % Allowed : 21.66 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.26), residues: 994 helix: 2.03 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 33 TYR 0.013 0.002 TYR B 51 PHE 0.011 0.001 PHE E 67 TRP 0.018 0.002 TRP L 70 HIS 0.007 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00455 (14877) covalent geometry : angle 0.61154 (21375) hydrogen bonds : bond 0.04821 ( 926) hydrogen bonds : angle 3.21314 ( 2354) metal coordination : bond 0.00713 ( 4) metal coordination : angle 1.85528 ( 3) *********************** 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 285 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.596 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: A 125 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8046 (mt0) REVERT: A 131 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: B 84 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7549 (mpp) REVERT: C 42 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7846 (mtp-110) REVERT: C 104 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7317 (mm-40) REVERT: K 103 LYS cc_start: 0.7994 (tppt) cc_final: 0.7688 (tppt) REVERT: L 38 GLN cc_start: 0.7523 (tp40) cc_final: 0.6913 (tp40) REVERT: M 38 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8135 (tm-30) outliers start: 32 outliers final: 22 residues processed: 261 average time/residue: 1.9757 time to fit residues: 546.9493 Evaluate side-chains 276 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 250 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 B residue 53 GLU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER 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 H residue 116 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 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 Chi-restraints excluded: chain M residue 26 MET Chi-restraints excluded: chain M residue 44 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.184259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.168689 restraints weight = 62165.711| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.19 r_work: 0.3656 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14881 Z= 0.243 Angle : 0.623 6.590 21378 Z= 0.377 Chirality : 0.042 0.162 2435 Planarity : 0.005 0.065 1696 Dihedral : 29.454 170.446 4332 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.92 % Allowed : 21.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.26), residues: 994 helix: 1.98 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 29 TYR 0.015 0.002 TYR B 51 PHE 0.019 0.002 PHE K 93 TRP 0.019 0.002 TRP L 70 HIS 0.008 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00541 (14877) covalent geometry : angle 0.62168 (21375) hydrogen bonds : bond 0.05084 ( 926) hydrogen bonds : angle 3.22220 ( 2354) metal coordination : bond 0.00686 ( 4) metal coordination : angle 2.93239 ( 3) *********************** 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 285 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 253 time to evaluate : 0.652 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 131 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7183 (mtp85) REVERT: C 104 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7360 (mm-40) REVERT: K 53 ASP cc_start: 0.6427 (OUTLIER) cc_final: 0.5622 (p0) REVERT: L 35 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7193 (mtt-85) REVERT: M 38 GLN cc_start: 0.8417 (mm-40) cc_final: 0.8162 (tm-30) outliers start: 32 outliers final: 25 residues processed: 263 average time/residue: 1.7902 time to fit residues: 498.8875 Evaluate side-chains 277 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 249 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 B residue 53 GLU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 87 SER 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 H residue 116 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 35 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 ILE Chi-restraints excluded: chain L residue 65 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.0970 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 73 ASN D 84 ASN K 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.180989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.166153 restraints weight = 62714.223| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.09 r_work: 0.3649 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14881 Z= 0.307 Angle : 0.666 7.402 21378 Z= 0.400 Chirality : 0.046 0.152 2435 Planarity : 0.006 0.060 1696 Dihedral : 29.530 172.039 4332 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.41 % Allowed : 22.64 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 994 helix: 1.76 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.31 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.015 0.002 TYR B 51 PHE 0.022 0.002 PHE K 93 TRP 0.022 0.002 TRP L 70 HIS 0.009 0.002 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00687 (14877) covalent geometry : angle 0.66448 (21375) hydrogen bonds : bond 0.05701 ( 926) hydrogen bonds : angle 3.37687 ( 2354) metal coordination : bond 0.01072 ( 4) metal coordination : angle 3.58119 ( 3) *********************** 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 295 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.564 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 125 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: A 131 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7190 (mtp85) REVERT: C 104 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7334 (mm-40) REVERT: K 132 ARG cc_start: 0.8045 (ttt90) cc_final: 0.7726 (ttt90) REVERT: M 38 GLN cc_start: 0.8458 (mm-40) cc_final: 0.8203 (tm-30) outliers start: 36 outliers final: 23 residues processed: 270 average time/residue: 1.7240 time to fit residues: 494.3392 Evaluate side-chains 281 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 B residue 53 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 87 SER 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 H residue 116 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 K residue 106 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 65 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 88 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 C 94 ASN D 84 ASN M 28 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.182287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.167328 restraints weight = 63078.460| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.09 r_work: 0.3666 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 0.041 14881 Z= 0.243 Angle : 0.637 7.461 21378 Z= 0.384 Chirality : 0.042 0.139 2435 Planarity : 0.006 0.055 1696 Dihedral : 29.510 170.895 4332 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.16 % Allowed : 23.13 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.26), residues: 994 helix: 1.89 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.23 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.014 0.002 TYR B 51 PHE 0.016 0.002 PHE K 93 TRP 0.019 0.002 TRP L 70 HIS 0.008 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00540 (14877) covalent geometry : angle 0.63659 (21375) hydrogen bonds : bond 0.05097 ( 926) hydrogen bonds : angle 3.28973 ( 2354) metal coordination : bond 0.00570 ( 4) metal coordination : angle 2.89944 ( 3) *********************** 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 292 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 258 time to evaluate : 0.503 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 125 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: A 131 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: C 104 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7353 (mm-40) REVERT: K 24 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.5165 (m110) REVERT: K 132 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7767 (ttt90) REVERT: L 31 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6994 (tm-30) REVERT: L 35 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7188 (mtt-85) REVERT: M 38 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8198 (tm-30) outliers start: 34 outliers final: 25 residues processed: 270 average time/residue: 1.6716 time to fit residues: 479.2151 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 : 0.531 ------------------------------------------------------------------------------- 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 B residue 53 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 87 SER 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 H residue 116 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 K residue 106 ARG Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 ILE 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 Chi-restraints excluded: chain M residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 101 optimal weight: 0.0970 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN 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 = 0.4071 r_free = 0.4071 target = 0.185183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.169850 restraints weight = 63488.732| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.15 r_work: 0.3677 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14881 Z= 0.180 Angle : 0.608 8.514 21378 Z= 0.368 Chirality : 0.038 0.151 2435 Planarity : 0.005 0.065 1696 Dihedral : 29.471 169.685 4332 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.06 % Allowed : 24.72 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.26), residues: 994 helix: 2.17 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.07 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.012 0.001 TYR B 51 PHE 0.013 0.001 PHE M 22 TRP 0.017 0.002 TRP M 33 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00397 (14877) covalent geometry : angle 0.60754 (21375) hydrogen bonds : bond 0.04463 ( 926) hydrogen bonds : angle 3.18612 ( 2354) metal coordination : bond 0.00449 ( 4) metal coordination : angle 2.45624 ( 3) *********************** 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 284 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 0.468 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: 0.8323 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 104 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7353 (mm-40) REVERT: G 36 LYS cc_start: 0.8322 (mptm) cc_final: 0.7967 (mptm) REVERT: K 132 ARG cc_start: 0.7967 (ttt90) cc_final: 0.7728 (ttt90) REVERT: L 31 GLU cc_start: 0.7194 (tm-30) cc_final: 0.6860 (tm-30) REVERT: L 35 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7104 (mtt-85) REVERT: M 38 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8131 (tm-30) outliers start: 25 outliers final: 20 residues processed: 264 average time/residue: 1.6550 time to fit residues: 463.5795 Evaluate side-chains 276 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 254 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU 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 H residue 116 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 K residue 106 ARG Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 47 LEU 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 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 73 ASN D 84 ASN K 111 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 = 0.4045 r_free = 0.4045 target = 0.182928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.168119 restraints weight = 62916.397| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.04 r_work: 0.3677 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14881 Z= 0.229 Angle : 0.636 8.536 21378 Z= 0.381 Chirality : 0.041 0.144 2435 Planarity : 0.005 0.070 1696 Dihedral : 29.451 170.383 4332 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.43 % Allowed : 24.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.26), residues: 994 helix: 2.07 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.12 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.013 0.002 TYR L 73 PHE 0.013 0.002 PHE E 67 TRP 0.020 0.003 TRP M 33 HIS 0.006 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00509 (14877) covalent geometry : angle 0.63519 (21375) hydrogen bonds : bond 0.04904 ( 926) hydrogen bonds : angle 3.25872 ( 2354) metal coordination : bond 0.00555 ( 4) metal coordination : angle 2.97877 ( 3) *********************** 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 281 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 253 time to evaluate : 0.710 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: A 125 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8070 (mt0) REVERT: A 131 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7157 (mtp85) REVERT: C 104 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7341 (mm-40) REVERT: K 132 ARG cc_start: 0.8023 (ttt90) cc_final: 0.7750 (ttt90) REVERT: L 31 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6899 (tm-30) REVERT: L 35 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7088 (mtt-85) REVERT: M 38 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8158 (tm-30) outliers start: 28 outliers final: 22 residues processed: 264 average time/residue: 1.9153 time to fit residues: 536.0803 Evaluate side-chains 277 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 252 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU 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 H residue 116 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 K residue 106 ARG Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 ILE 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 50 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4055 r_free = 0.4055 target = 0.183749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.168920 restraints weight = 63087.488| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.04 r_work: 0.3670 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.005 0.041 14881 Z= 0.205 Angle : 0.633 11.483 21378 Z= 0.378 Chirality : 0.040 0.166 2435 Planarity : 0.005 0.075 1696 Dihedral : 29.448 169.968 4332 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.18 % Allowed : 25.46 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.26), residues: 994 helix: 2.15 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.10 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 33 TYR 0.012 0.002 TYR B 51 PHE 0.012 0.002 PHE M 22 TRP 0.027 0.003 TRP K 25 HIS 0.006 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00454 (14877) covalent geometry : angle 0.63221 (21375) hydrogen bonds : bond 0.04663 ( 926) hydrogen bonds : angle 3.23549 ( 2354) metal coordination : bond 0.00509 ( 4) metal coordination : angle 2.87511 ( 3) ********************** 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 281 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 255 time to evaluate : 0.614 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: 0.8326 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: A 131 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7163 (mtp85) REVERT: C 104 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7348 (mm-40) REVERT: G 36 LYS cc_start: 0.8321 (mptm) cc_final: 0.7963 (mptm) REVERT: K 103 LYS cc_start: 0.7820 (tppt) cc_final: 0.7273 (tppt) REVERT: K 132 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7731 (ttt90) REVERT: L 31 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6878 (tm-30) REVERT: L 35 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.7028 (mtt-85) REVERT: M 38 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8147 (tm-30) outliers start: 26 outliers final: 21 residues processed: 264 average time/residue: 2.0445 time to fit residues: 571.0280 Evaluate side-chains 278 residues out of total 867 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 A residue 133 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 71 GLU 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 H residue 116 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 K residue 106 ARG Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 ILE 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 116 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 109 optimal weight: 0.3980 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN 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 = 0.4061 r_free = 0.4061 target = 0.184235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.168809 restraints weight = 62586.961| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.15 r_work: 0.3673 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.3150 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= 0.193 Angle : 0.632 12.144 21378 Z= 0.376 Chirality : 0.039 0.172 2435 Planarity : 0.005 0.075 1696 Dihedral : 29.443 169.756 4332 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.30 % Allowed : 25.21 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.99 (0.26), residues: 994 helix: 2.18 (0.19), residues: 718 sheet: None (None), residues: 0 loop : -1.07 (0.32), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 33 TYR 0.011 0.001 TYR B 51 PHE 0.017 0.002 PHE M 22 TRP 0.032 0.004 TRP K 25 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd covalent geometry : bond 0.00428 (14877) covalent geometry : angle 0.63066 (21375) hydrogen bonds : bond 0.04568 ( 926) hydrogen bonds : angle 3.21927 ( 2354) metal coordination : bond 0.00412 ( 4) metal coordination : angle 2.84803 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12624.83 seconds wall clock time: 213 minutes 44.07 seconds (12824.07 seconds total)