Starting phenix.real_space_refine on Thu Aug 6 09:38:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iej_35383/08_2026/8iej_35383.map" } resolution = 3.12 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= 0.000 sd= 0.002 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 1067 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 35 5.16 5 C 7937 2.51 5 N 2635 2.21 5 O 3181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "R" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1067 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 135} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 4, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12108 SG CYS A 948 47.191 47.637 12.094 1.00216.57 S ATOM 12259 SG CYS A 968 47.274 50.753 11.972 1.00213.80 S ATOM 12285 SG CYS A 971 44.012 50.383 11.912 1.00208.87 S ATOM 12214 SG CYS A 963 43.787 45.876 27.411 1.00197.39 S ATOM 12386 SG CYS A 983 41.373 46.465 23.589 1.00200.37 S ATOM 12587 SG CYS M 922 63.805 58.535 26.486 1.00185.29 S ATOM 12606 SG CYS M 925 67.390 57.651 27.123 1.00189.09 S ATOM 12746 SG CYS M 942 64.428 55.921 29.187 1.00161.27 S ATOM 12772 SG CYS M 945 65.569 58.880 30.124 1.00148.39 S ATOM 12701 SG CYS M 937 53.818 64.915 26.888 1.00146.39 S ATOM 12879 SG CYS M 957 57.040 66.699 27.510 1.00142.03 S ATOM 12901 SG CYS M 960 54.070 68.660 26.301 1.00148.06 S Time building chain proxies: 2.99, per 1000 atoms: 0.21 Number of scatterers: 14086 At special positions: 0 Unit cell: (120.288, 121.362, 113.844, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 35 16.00 P 294 15.00 O 3181 8.00 N 2635 7.00 C 7937 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 345.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 948 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 971 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 968 " pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 965 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 983 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 963 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 945 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 942 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 925 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 922 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 939 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 957 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 960 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 937 " Number of angles added : 9 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 62.2% alpha, 5.0% beta 140 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.473A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.542A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 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 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.874A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.786A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.535A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.425A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain '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 103 through 124 removed outlier: 3.605A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.557A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.171A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'A' and resid 942 through 947 Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'M' and resid 916 through 920 Processing helix chain 'M' and resid 942 through 952 Processing helix chain 'R' and resid 3 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 123 through 133 Processing helix chain 'R' and resid 133 through 149 removed outlier: 3.562A pdb=" N TRP R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.192A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.822A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.924A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.395A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.791A pdb=" N THR G 101 " --> pdb=" O TYR L 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.809A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967 removed outlier: 4.103A pdb=" N VAL A 959 " --> pdb=" O HIS A 996 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 996 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 939 through 941 removed outlier: 3.727A pdb=" N HIS M 939 " --> pdb=" O LEU M 934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 28 483 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3044 1.33 - 1.45: 4483 1.45 - 1.57: 6786 1.57 - 1.69: 586 1.69 - 1.81: 48 Bond restraints: 14947 Sorted by residual: bond pdb=" C3' DG I -4 " pdb=" O3' DG I -4 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC J 8 " pdb=" O3' DC J 8 " ideal model delta sigma weight residual 1.435 1.394 0.041 1.30e-02 5.92e+03 9.82e+00 bond pdb=" C3' DT J 64 " pdb=" C2' DT J 64 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.95e+00 ... (remaining 14942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 21246 2.62 - 5.25: 205 5.25 - 7.87: 12 7.87 - 10.50: 1 10.50 - 13.12: 1 Bond angle restraints: 21465 Sorted by residual: angle pdb=" N ARG A 981 " pdb=" CA ARG A 981 " pdb=" C ARG A 981 " ideal model delta sigma weight residual 108.17 95.05 13.12 1.85e+00 2.92e-01 5.03e+01 angle pdb=" O4' DC I -26 " pdb=" C4' DC I -26 " pdb=" C3' DC I -26 " ideal model delta sigma weight residual 106.00 102.73 3.27 6.00e-01 2.78e+00 2.97e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT J 30 " pdb=" C4 DT J 30 " pdb=" O4 DT J 30 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 ... (remaining 21460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 6767 34.03 - 68.06: 1449 68.06 - 102.10: 15 102.10 - 136.13: 1 136.13 - 170.16: 3 Dihedral angle restraints: 8235 sinusoidal: 5233 harmonic: 3002 Sorted by residual: dihedral pdb=" CA ARG M 928 " pdb=" C ARG M 928 " pdb=" N LYS M 929 " pdb=" CA LYS M 929 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO R 28 " pdb=" C PRO R 28 " pdb=" N SER R 29 " pdb=" CA SER R 29 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 49.84 170.16 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1921 0.059 - 0.119: 467 0.119 - 0.178: 41 0.178 - 0.237: 2 0.237 - 0.296: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CA ARG A 981 " pdb=" N ARG A 981 " pdb=" C ARG A 981 " pdb=" CB ARG A 981 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.51 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG A 979 " pdb=" N ARG A 979 " pdb=" C ARG A 979 " pdb=" CB ARG A 979 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-01 ... (remaining 2429 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.025 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR D 83 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 36 " -0.020 2.00e-02 2.50e+03 1.82e-02 8.26e+00 pdb=" CG TRP R 36 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP R 36 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 36 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 36 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 36 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 DA I 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.001 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3438 2.81 - 3.51: 20074 3.51 - 4.20: 39166 4.20 - 4.90: 58629 Nonbonded interactions: 121310 Sorted by model distance: nonbonded pdb=" OH TYR A 999 " pdb=" NE2 HIS M 939 " model vdw 1.421 3.120 nonbonded pdb=" OH TYR A 999 " pdb=" CD2 HIS M 939 " model vdw 1.627 3.260 nonbonded pdb=" NH2 ARG A 954 " pdb=" SG CYS A 971 " model vdw 2.095 3.480 nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.132 3.040 nonbonded pdb=" OG SER R 29 " pdb=" O ASN R 32 " model vdw 2.136 3.040 ... (remaining 121305 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 942 through 952 or resid 954 through 972 or resid 975 thro \ ugh 976 or resid 979 through 992 or resid 994 through 1102)) selection = (chain 'M' and (resid 916 through 925 or (resid 926 and (name N or name CA or na \ me C or name O or name CB )) or resid 928 through 929 or (resid 930 and (name N \ or name CA or name C or name O or name CB )) or resid 931 through 946 or resid 9 \ 49 through 950 or resid 953 through 966 or resid 968 through 973 or (resid 974 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1001 through 10 \ 02)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 119 or resid 121 through 124)) selection = (chain 'H' and (resid 31 through 119 or resid 121 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.27 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.310 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 : 0.011 0.585 14963 Z= 0.689 Angle : 0.791 18.310 21474 Z= 0.642 Chirality : 0.049 0.296 2432 Planarity : 0.005 0.066 1710 Dihedral : 26.500 170.160 6293 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.32 % Allowed : 0.60 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.90 (0.27), residues: 1008 helix: 2.04 (0.21), residues: 641 sheet: 0.59 (1.02), residues: 27 loop : -0.17 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 11 TYR 0.074 0.002 TYR D 83 PHE 0.020 0.002 PHE M 941 TRP 0.048 0.005 TRP R 36 HIS 0.006 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00670 / 0.55 (14947) covalent geometry : angle 0.77238 / 0.64 (21465) hydrogen bonds : bond 0.09008 / 5.89 ( 844) hydrogen bonds : angle 3.88644 / 2.76 ( 2146) metal coordination : bond 0.24229 / 14.96 ( 14) metal coordination : angle 8.34178 / 4.74 ( 9) Misc. bond : bond 0.29501 / 14.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 0.264 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: C 38 ASN cc_start: 0.8421 (t0) cc_final: 0.8127 (p0) REVERT: C 72 ASP cc_start: 0.8554 (m-30) cc_final: 0.8333 (m-30) REVERT: C 90 ASP cc_start: 0.8660 (t70) cc_final: 0.8449 (t0) REVERT: D 68 ASP cc_start: 0.8827 (t70) cc_final: 0.8595 (t0) REVERT: G 24 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8961 (mm-40) REVERT: G 38 ASN cc_start: 0.8356 (t0) cc_final: 0.7963 (t0) REVERT: G 90 ASP cc_start: 0.8512 (t70) cc_final: 0.8301 (t70) REVERT: K 56 LYS cc_start: 0.9346 (ttmm) cc_final: 0.9120 (ttpp) REVERT: K 59 GLU cc_start: 0.8637 (pm20) cc_final: 0.8309 (pm20) REVERT: A 972 VAL cc_start: 0.9370 (m) cc_final: 0.9048 (m) REVERT: A 996 HIS cc_start: 0.6472 (t-90) cc_final: 0.6202 (t-90) REVERT: M 938 PHE cc_start: 0.9013 (m-80) cc_final: 0.8619 (m-80) REVERT: M 967 ASN cc_start: 0.9247 (m-40) cc_final: 0.8770 (m-40) REVERT: R 36 TRP cc_start: 0.6377 (m100) cc_final: 0.5977 (m100) outliers start: 11 outliers final: 8 residues processed: 265 average time/residue: 0.1099 time to fit residues: 40.5119 Evaluate side-chains 236 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN C 104 GLN G 73 ASN K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.083376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.049988 restraints weight = 47898.177| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.56 r_work: 0.2612 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14963 Z= 0.187 Angle : 0.697 20.730 21474 Z= 0.388 Chirality : 0.046 0.291 2432 Planarity : 0.005 0.062 1710 Dihedral : 29.826 170.688 4379 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.80 % Allowed : 10.22 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.92 (0.27), residues: 1008 helix: 2.14 (0.21), residues: 644 sheet: -0.21 (0.85), residues: 37 loop : -0.28 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 979 TYR 0.023 0.002 TYR H 83 PHE 0.021 0.002 PHE R 13 TRP 0.009 0.002 TRP R 36 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (14947) covalent geometry : angle 0.67137 / 0.39 (21465) hydrogen bonds : bond 0.04880 / 3.18 ( 844) hydrogen bonds : angle 3.37452 / 2.38 ( 2146) metal coordination : bond 0.01411 / 1.11 ( 14) metal coordination : angle 9.20482 / 5.24 ( 9) Misc. bond : bond 0.00633 / 0.30 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 252 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8877 (t70) cc_final: 0.8659 (t70) REVERT: D 68 ASP cc_start: 0.9390 (t70) cc_final: 0.9136 (t0) REVERT: E 59 GLU cc_start: 0.9070 (pm20) cc_final: 0.8802 (pm20) REVERT: G 36 LYS cc_start: 0.8948 (tmtt) cc_final: 0.8691 (tmtt) REVERT: G 38 ASN cc_start: 0.8487 (t0) cc_final: 0.8277 (t0) REVERT: G 73 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8793 (t0) REVERT: G 90 ASP cc_start: 0.8769 (t70) cc_final: 0.8432 (t70) REVERT: H 42 TYR cc_start: 0.9016 (t80) cc_final: 0.8640 (t80) REVERT: K 56 LYS cc_start: 0.9383 (ttmm) cc_final: 0.9159 (ttpp) REVERT: K 59 GLU cc_start: 0.8897 (pm20) cc_final: 0.8484 (pm20) REVERT: A 962 LYS cc_start: 0.8585 (mtmt) cc_final: 0.8322 (mtmm) REVERT: M 926 ASN cc_start: 0.9247 (m110) cc_final: 0.8849 (m110) REVERT: M 947 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9224 (tppt) REVERT: M 951 ASP cc_start: 0.9266 (m-30) cc_final: 0.8795 (p0) REVERT: M 967 ASN cc_start: 0.9257 (m-40) cc_final: 0.8756 (m-40) outliers start: 15 outliers final: 9 residues processed: 258 average time/residue: 0.1281 time to fit residues: 45.7460 Evaluate side-chains 247 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 40.0000 chunk 94 optimal weight: 0.6980 chunk 65 optimal weight: 20.0000 chunk 64 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN K 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.083748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050486 restraints weight = 47698.680| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.57 r_work: 0.2623 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14963 Z= 0.158 Angle : 0.653 17.709 21474 Z= 0.369 Chirality : 0.045 0.268 2432 Planarity : 0.005 0.061 1710 Dihedral : 29.776 170.356 4373 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.68 % Allowed : 12.86 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 2.01 (0.27), residues: 1008 helix: 2.23 (0.21), residues: 644 sheet: 0.04 (0.83), residues: 39 loop : -0.32 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 973 TYR 0.029 0.002 TYR D 83 PHE 0.015 0.002 PHE A 969 TRP 0.011 0.002 TRP R 36 HIS 0.011 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (14947) covalent geometry : angle 0.62893 / 0.37 (21465) hydrogen bonds : bond 0.04467 / 2.93 ( 844) hydrogen bonds : angle 3.18851 / 2.26 ( 2146) metal coordination : bond 0.00904 / 0.70 ( 14) metal coordination : angle 8.65683 / 4.93 ( 9) Misc. bond : bond 0.00161 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 251 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8851 (t70) cc_final: 0.8603 (t70) REVERT: D 68 ASP cc_start: 0.9396 (t70) cc_final: 0.9147 (t0) REVERT: E 59 GLU cc_start: 0.9107 (pm20) cc_final: 0.8822 (pm20) REVERT: G 73 ASN cc_start: 0.9024 (t160) cc_final: 0.8760 (t0) REVERT: G 90 ASP cc_start: 0.8707 (t70) cc_final: 0.8366 (t0) REVERT: H 42 TYR cc_start: 0.8898 (t80) cc_final: 0.8496 (t80) REVERT: K 56 LYS cc_start: 0.9380 (ttmm) cc_final: 0.9149 (ttpp) REVERT: K 59 GLU cc_start: 0.8891 (pm20) cc_final: 0.8476 (pm20) REVERT: A 962 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8344 (mtmm) REVERT: M 926 ASN cc_start: 0.9192 (m110) cc_final: 0.8909 (m110) REVERT: M 936 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8629 (tptt) REVERT: M 938 PHE cc_start: 0.9232 (m-80) cc_final: 0.8838 (m-80) REVERT: M 951 ASP cc_start: 0.9223 (m-30) cc_final: 0.8745 (p0) REVERT: M 967 ASN cc_start: 0.9216 (m-40) cc_final: 0.8573 (m-40) REVERT: M 968 ASP cc_start: 0.9377 (m-30) cc_final: 0.8195 (t0) REVERT: R 12 ASP cc_start: 0.8418 (m-30) cc_final: 0.7853 (m-30) outliers start: 14 outliers final: 7 residues processed: 257 average time/residue: 0.1299 time to fit residues: 46.2185 Evaluate side-chains 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 237 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.084180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.051189 restraints weight = 47629.764| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.55 r_work: 0.2641 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14963 Z= 0.142 Angle : 0.639 15.844 21474 Z= 0.363 Chirality : 0.044 0.252 2432 Planarity : 0.005 0.113 1710 Dihedral : 29.729 170.162 4361 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.80 % Allowed : 13.10 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 2.03 (0.27), residues: 1008 helix: 2.27 (0.21), residues: 644 sheet: 0.21 (0.86), residues: 39 loop : -0.40 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG A 981 TYR 0.037 0.002 TYR D 83 PHE 0.015 0.001 PHE R 13 TRP 0.011 0.002 TRP R 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (14947) covalent geometry : angle 0.61693 / 0.36 (21465) hydrogen bonds : bond 0.04217 / 2.76 ( 844) hydrogen bonds : angle 3.11467 / 2.21 ( 2146) metal coordination : bond 0.00636 / 0.54 ( 14) metal coordination : angle 8.22715 / 4.64 ( 9) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9636 (mt) cc_final: 0.9398 (tt) REVERT: C 72 ASP cc_start: 0.8769 (m-30) cc_final: 0.8566 (m-30) REVERT: C 90 ASP cc_start: 0.8785 (t70) cc_final: 0.8520 (t70) REVERT: D 68 ASP cc_start: 0.9396 (t70) cc_final: 0.9124 (t0) REVERT: E 59 GLU cc_start: 0.9110 (pm20) cc_final: 0.8870 (pm20) REVERT: G 73 ASN cc_start: 0.8955 (t160) cc_final: 0.8520 (t0) REVERT: G 90 ASP cc_start: 0.8629 (t70) cc_final: 0.8253 (t0) REVERT: H 42 TYR cc_start: 0.8895 (t80) cc_final: 0.8475 (t80) REVERT: K 56 LYS cc_start: 0.9387 (ttmm) cc_final: 0.9137 (ttpp) REVERT: K 59 GLU cc_start: 0.8886 (pm20) cc_final: 0.8467 (pm20) REVERT: A 962 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8320 (mtmm) REVERT: A 969 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: A 996 HIS cc_start: 0.6834 (t-90) cc_final: 0.6609 (t-170) REVERT: M 936 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8684 (tptt) REVERT: M 938 PHE cc_start: 0.9234 (m-80) cc_final: 0.8691 (m-80) REVERT: M 951 ASP cc_start: 0.9184 (m-30) cc_final: 0.8776 (p0) REVERT: M 967 ASN cc_start: 0.9125 (m-40) cc_final: 0.8714 (m-40) REVERT: M 968 ASP cc_start: 0.9354 (m-30) cc_final: 0.8286 (t0) REVERT: R 16 LEU cc_start: 0.5724 (tt) cc_final: 0.5454 (pp) REVERT: R 80 ASN cc_start: 0.8310 (t0) cc_final: 0.7383 (t0) outliers start: 15 outliers final: 10 residues processed: 263 average time/residue: 0.1293 time to fit residues: 47.4389 Evaluate side-chains 251 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 67 optimal weight: 40.0000 chunk 73 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN K 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.082679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049435 restraints weight = 47817.279| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.57 r_work: 0.2585 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14963 Z= 0.245 Angle : 0.705 19.117 21474 Z= 0.387 Chirality : 0.046 0.252 2432 Planarity : 0.005 0.101 1710 Dihedral : 29.880 170.267 4361 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.28 % Allowed : 14.54 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.98 (0.27), residues: 1008 helix: 2.17 (0.20), residues: 646 sheet: 0.51 (0.94), residues: 37 loop : -0.32 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 981 TYR 0.064 0.002 TYR H 83 PHE 0.022 0.002 PHE R 13 TRP 0.008 0.002 TRP R 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (14947) covalent geometry : angle 0.67795 / 0.38 (21465) hydrogen bonds : bond 0.05022 / 3.32 ( 844) hydrogen bonds : angle 3.26093 / 2.32 ( 2146) metal coordination : bond 0.01067 / 0.86 ( 14) metal coordination : angle 9.54763 / 5.39 ( 9) Misc. bond : bond 0.00475 / 0.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9639 (mt) cc_final: 0.9401 (tt) REVERT: C 90 ASP cc_start: 0.8873 (t70) cc_final: 0.8607 (t70) REVERT: D 68 ASP cc_start: 0.9413 (t70) cc_final: 0.9170 (t0) REVERT: E 59 GLU cc_start: 0.9110 (pm20) cc_final: 0.8834 (pm20) REVERT: F 88 TYR cc_start: 0.9307 (m-10) cc_final: 0.8946 (m-10) REVERT: G 73 ASN cc_start: 0.8936 (t160) cc_final: 0.8660 (t0) REVERT: G 90 ASP cc_start: 0.8630 (t70) cc_final: 0.8259 (t0) REVERT: H 42 TYR cc_start: 0.8946 (t80) cc_final: 0.8554 (t80) REVERT: K 56 LYS cc_start: 0.9421 (ttmm) cc_final: 0.9161 (ttpp) REVERT: K 59 GLU cc_start: 0.8901 (pm20) cc_final: 0.8458 (pm20) REVERT: A 962 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8424 (mtmm) REVERT: A 969 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: A 979 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7192 (tpt90) REVERT: A 996 HIS cc_start: 0.7040 (t-90) cc_final: 0.6755 (t-170) REVERT: M 936 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8780 (tptt) REVERT: M 938 PHE cc_start: 0.9229 (m-80) cc_final: 0.8644 (m-80) REVERT: M 951 ASP cc_start: 0.9231 (m-30) cc_final: 0.8823 (p0) REVERT: M 967 ASN cc_start: 0.9222 (m-40) cc_final: 0.8825 (m-40) REVERT: M 968 ASP cc_start: 0.9388 (m-30) cc_final: 0.8174 (t0) outliers start: 19 outliers final: 11 residues processed: 251 average time/residue: 0.1224 time to fit residues: 42.9162 Evaluate side-chains 242 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 0.9980 chunk 115 optimal weight: 0.2980 chunk 96 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.084000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051163 restraints weight = 47753.302| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.56 r_work: 0.2638 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14963 Z= 0.141 Angle : 0.662 24.070 21474 Z= 0.366 Chirality : 0.044 0.256 2432 Planarity : 0.005 0.122 1710 Dihedral : 29.808 169.728 4361 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.16 % Allowed : 15.87 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 2.09 (0.27), residues: 1008 helix: 2.29 (0.21), residues: 644 sheet: 0.97 (0.98), residues: 37 loop : -0.40 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG A 981 TYR 0.056 0.002 TYR D 83 PHE 0.027 0.001 PHE R 13 TRP 0.023 0.003 TRP R 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (14947) covalent geometry : angle 0.62569 / 0.36 (21465) hydrogen bonds : bond 0.04124 / 2.70 ( 844) hydrogen bonds : angle 3.05651 / 2.17 ( 2146) metal coordination : bond 0.00753 / 0.53 ( 14) metal coordination : angle 10.64284 / 6.01 ( 9) Misc. bond : bond 0.00033 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9279 (m-40) cc_final: 0.8968 (t0) REVERT: C 90 ASP cc_start: 0.8865 (t70) cc_final: 0.8561 (t0) REVERT: D 68 ASP cc_start: 0.9400 (t70) cc_final: 0.9152 (t0) REVERT: E 59 GLU cc_start: 0.9130 (pm20) cc_final: 0.8866 (pm20) REVERT: G 73 ASN cc_start: 0.8891 (t160) cc_final: 0.8587 (t0) REVERT: G 90 ASP cc_start: 0.8645 (t70) cc_final: 0.8251 (t0) REVERT: H 42 TYR cc_start: 0.8875 (t80) cc_final: 0.8509 (t80) REVERT: K 56 LYS cc_start: 0.9391 (ttmm) cc_final: 0.9140 (ttpp) REVERT: K 59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8439 (pm20) REVERT: A 969 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: M 936 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8797 (tptt) REVERT: M 938 PHE cc_start: 0.9177 (m-80) cc_final: 0.8557 (m-80) REVERT: M 951 ASP cc_start: 0.9176 (m-30) cc_final: 0.8760 (p0) REVERT: M 967 ASN cc_start: 0.9204 (m-40) cc_final: 0.8810 (m-40) REVERT: M 968 ASP cc_start: 0.9306 (m-30) cc_final: 0.8238 (t0) REVERT: R 49 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8363 (mm-30) outliers start: 18 outliers final: 13 residues processed: 267 average time/residue: 0.1337 time to fit residues: 49.7842 Evaluate side-chains 260 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 245 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.049289 restraints weight = 47829.677| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.55 r_work: 0.2589 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2585 r_free = 0.2585 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14963 Z= 0.228 Angle : 0.714 23.952 21474 Z= 0.388 Chirality : 0.046 0.238 2432 Planarity : 0.005 0.055 1710 Dihedral : 29.923 169.850 4361 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.92 % Allowed : 17.31 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.96 (0.27), residues: 1008 helix: 2.17 (0.21), residues: 646 sheet: 1.31 (1.16), residues: 27 loop : -0.43 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 979 TYR 0.080 0.003 TYR D 83 PHE 0.026 0.002 PHE R 13 TRP 0.020 0.003 TRP R 36 HIS 0.024 0.002 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (14947) covalent geometry : angle 0.68200 / 0.39 (21465) hydrogen bonds : bond 0.05004 / 3.31 ( 844) hydrogen bonds : angle 3.23310 / 2.30 ( 2146) metal coordination : bond 0.01035 / 0.71 ( 14) metal coordination : angle 10.41949 / 5.91 ( 9) Misc. bond : bond 0.00316 / 0.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9319 (m-40) cc_final: 0.8996 (t0) REVERT: C 90 ASP cc_start: 0.8921 (t70) cc_final: 0.8652 (t70) REVERT: D 68 ASP cc_start: 0.9406 (t70) cc_final: 0.9174 (t0) REVERT: E 59 GLU cc_start: 0.9128 (pm20) cc_final: 0.8846 (pm20) REVERT: G 73 ASN cc_start: 0.8989 (t160) cc_final: 0.8757 (t0) REVERT: G 90 ASP cc_start: 0.8636 (t70) cc_final: 0.8275 (t0) REVERT: H 42 TYR cc_start: 0.8920 (t80) cc_final: 0.8572 (t80) REVERT: K 56 LYS cc_start: 0.9424 (ttmm) cc_final: 0.9168 (ttpp) REVERT: K 59 GLU cc_start: 0.8906 (pm20) cc_final: 0.8460 (pm20) REVERT: A 969 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: M 936 LYS cc_start: 0.9052 (tptm) cc_final: 0.8703 (tptt) REVERT: M 938 PHE cc_start: 0.9264 (m-80) cc_final: 0.8856 (m-80) REVERT: M 951 ASP cc_start: 0.9224 (m-30) cc_final: 0.8775 (p0) REVERT: M 967 ASN cc_start: 0.9245 (m-40) cc_final: 0.8820 (m-40) REVERT: M 968 ASP cc_start: 0.9324 (m-30) cc_final: 0.8113 (t0) REVERT: R 36 TRP cc_start: 0.7370 (m100) cc_final: 0.7149 (m100) REVERT: R 101 ASP cc_start: 0.8497 (p0) cc_final: 0.7917 (m-30) outliers start: 16 outliers final: 11 residues processed: 247 average time/residue: 0.1336 time to fit residues: 46.0492 Evaluate side-chains 245 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 933 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.083127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050157 restraints weight = 47767.088| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.61 r_work: 0.2614 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2609 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2609 r_free = 0.2609 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2609 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14963 Z= 0.169 Angle : 0.680 21.452 21474 Z= 0.376 Chirality : 0.045 0.248 2432 Planarity : 0.005 0.080 1710 Dihedral : 29.924 169.503 4357 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.56 % Allowed : 17.79 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.96 (0.27), residues: 1008 helix: 2.19 (0.21), residues: 644 sheet: 1.10 (1.07), residues: 29 loop : -0.45 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 979 TYR 0.081 0.002 TYR D 83 PHE 0.019 0.001 PHE R 13 TRP 0.013 0.002 TRP R 36 HIS 0.016 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (14947) covalent geometry : angle 0.65158 / 0.37 (21465) hydrogen bonds : bond 0.04345 / 2.85 ( 844) hydrogen bonds : angle 3.15187 / 2.24 ( 2146) metal coordination : bond 0.00671 / 0.49 ( 14) metal coordination : angle 9.54054 / 5.40 ( 9) Misc. bond : bond 0.00079 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9297 (m-40) cc_final: 0.8987 (t0) REVERT: C 90 ASP cc_start: 0.8929 (t70) cc_final: 0.8636 (t70) REVERT: D 68 ASP cc_start: 0.9403 (t70) cc_final: 0.9165 (t0) REVERT: E 59 GLU cc_start: 0.9149 (pm20) cc_final: 0.8878 (pm20) REVERT: G 73 ASN cc_start: 0.9012 (t160) cc_final: 0.8722 (t0) REVERT: G 90 ASP cc_start: 0.8664 (t70) cc_final: 0.8278 (t0) REVERT: H 42 TYR cc_start: 0.8882 (t80) cc_final: 0.8538 (t80) REVERT: K 56 LYS cc_start: 0.9419 (ttmm) cc_final: 0.9169 (ttpp) REVERT: K 59 GLU cc_start: 0.8853 (pm20) cc_final: 0.8429 (pm20) REVERT: A 969 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: M 936 LYS cc_start: 0.9039 (tptm) cc_final: 0.8742 (tptt) REVERT: M 938 PHE cc_start: 0.9235 (m-80) cc_final: 0.8756 (m-80) REVERT: M 951 ASP cc_start: 0.9199 (m-30) cc_final: 0.8771 (p0) REVERT: M 955 ARG cc_start: 0.8106 (mtm-85) cc_final: 0.7089 (mtm-85) REVERT: M 967 ASN cc_start: 0.9247 (m-40) cc_final: 0.8819 (m-40) REVERT: M 968 ASP cc_start: 0.9289 (m-30) cc_final: 0.8104 (t0) REVERT: R 36 TRP cc_start: 0.7376 (m100) cc_final: 0.7054 (m100) REVERT: R 101 ASP cc_start: 0.8440 (p0) cc_final: 0.7856 (m-30) outliers start: 13 outliers final: 11 residues processed: 257 average time/residue: 0.1362 time to fit residues: 48.9778 Evaluate side-chains 255 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 243 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 60 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.049596 restraints weight = 47920.278| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.62 r_work: 0.2599 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14963 Z= 0.204 Angle : 0.709 21.695 21474 Z= 0.388 Chirality : 0.046 0.238 2432 Planarity : 0.005 0.075 1710 Dihedral : 29.971 169.344 4357 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.68 % Allowed : 18.27 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.84 (0.27), residues: 1008 helix: 2.13 (0.21), residues: 645 sheet: -0.36 (0.89), residues: 42 loop : -0.44 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 979 TYR 0.082 0.002 TYR D 83 PHE 0.018 0.002 PHE R 13 TRP 0.012 0.002 TRP R 36 HIS 0.014 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (14947) covalent geometry : angle 0.68126 / 0.39 (21465) hydrogen bonds : bond 0.04725 / 3.12 ( 844) hydrogen bonds : angle 3.23116 / 2.30 ( 2146) metal coordination : bond 0.00835 / 0.60 ( 14) metal coordination : angle 9.69055 / 5.48 ( 9) Misc. bond : bond 0.00191 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9300 (m-40) cc_final: 0.8985 (t0) REVERT: C 90 ASP cc_start: 0.8995 (t70) cc_final: 0.8684 (t70) REVERT: D 68 ASP cc_start: 0.9407 (t70) cc_final: 0.9171 (t0) REVERT: E 59 GLU cc_start: 0.9146 (pm20) cc_final: 0.8864 (pm20) REVERT: G 73 ASN cc_start: 0.9049 (t160) cc_final: 0.8748 (t0) REVERT: G 90 ASP cc_start: 0.8669 (t70) cc_final: 0.8298 (t0) REVERT: H 42 TYR cc_start: 0.8901 (t80) cc_final: 0.8560 (t80) REVERT: H 93 GLU cc_start: 0.8829 (mp0) cc_final: 0.8598 (mp0) REVERT: K 56 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9166 (ttpp) REVERT: K 59 GLU cc_start: 0.8853 (pm20) cc_final: 0.8423 (pm20) REVERT: A 969 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 996 HIS cc_start: 0.6524 (t-170) cc_final: 0.6186 (t-170) REVERT: M 936 LYS cc_start: 0.9015 (tptm) cc_final: 0.8767 (tptt) REVERT: M 938 PHE cc_start: 0.9232 (m-80) cc_final: 0.8672 (m-80) REVERT: M 951 ASP cc_start: 0.9234 (m-30) cc_final: 0.8760 (p0) REVERT: M 955 ARG cc_start: 0.8164 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: M 967 ASN cc_start: 0.9240 (m-40) cc_final: 0.8797 (m-40) REVERT: M 968 ASP cc_start: 0.9293 (m-30) cc_final: 0.8090 (t0) REVERT: R 36 TRP cc_start: 0.7428 (m100) cc_final: 0.6921 (m100) outliers start: 14 outliers final: 12 residues processed: 253 average time/residue: 0.1328 time to fit residues: 46.6829 Evaluate side-chains 253 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 240 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 15 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 30.0000 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.083886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051149 restraints weight = 47518.309| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.61 r_work: 0.2642 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14963 Z= 0.142 Angle : 0.678 19.769 21474 Z= 0.377 Chirality : 0.044 0.253 2432 Planarity : 0.005 0.050 1710 Dihedral : 29.886 168.936 4357 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.92 % Allowed : 18.87 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.93 (0.27), residues: 1008 helix: 2.21 (0.21), residues: 643 sheet: 1.73 (1.07), residues: 27 loop : -0.60 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 979 TYR 0.068 0.002 TYR D 83 PHE 0.017 0.002 PHE R 13 TRP 0.014 0.002 TRP R 36 HIS 0.014 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (14947) covalent geometry : angle 0.65270 / 0.38 (21465) hydrogen bonds : bond 0.04135 / 2.72 ( 844) hydrogen bonds : angle 3.13908 / 2.23 ( 2146) metal coordination : bond 0.00684 / 0.52 ( 14) metal coordination : angle 9.00310 / 5.09 ( 9) Misc. bond : bond 0.00140 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 255 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9239 (m-40) cc_final: 0.8971 (t0) REVERT: C 90 ASP cc_start: 0.8966 (t70) cc_final: 0.8610 (t70) REVERT: D 68 ASP cc_start: 0.9419 (t70) cc_final: 0.9143 (t0) REVERT: D 79 ARG cc_start: 0.8694 (ttm-80) cc_final: 0.8494 (ttm-80) REVERT: E 59 GLU cc_start: 0.9134 (pm20) cc_final: 0.8861 (pm20) REVERT: G 73 ASN cc_start: 0.9031 (OUTLIER) cc_final: 0.8721 (t0) REVERT: G 90 ASP cc_start: 0.8602 (t70) cc_final: 0.8204 (t0) REVERT: H 42 TYR cc_start: 0.8852 (t80) cc_final: 0.8523 (t80) REVERT: K 56 LYS cc_start: 0.9387 (ttmm) cc_final: 0.9134 (ttpp) REVERT: K 59 GLU cc_start: 0.8817 (pm20) cc_final: 0.8436 (pm20) REVERT: A 969 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: A 996 HIS cc_start: 0.6664 (t-170) cc_final: 0.6375 (t-170) REVERT: M 938 PHE cc_start: 0.9240 (m-80) cc_final: 0.8652 (m-80) REVERT: M 951 ASP cc_start: 0.9207 (m-30) cc_final: 0.8746 (p0) REVERT: M 967 ASN cc_start: 0.9253 (m-40) cc_final: 0.8965 (m-40) REVERT: R 36 TRP cc_start: 0.7439 (m100) cc_final: 0.6920 (m100) REVERT: R 62 GLU cc_start: 0.6124 (pp20) cc_final: 0.5457 (pp20) outliers start: 16 outliers final: 12 residues processed: 263 average time/residue: 0.1360 time to fit residues: 49.9541 Evaluate side-chains 256 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050991 restraints weight = 47640.848| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.60 r_work: 0.2638 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14963 Z= 0.158 Angle : 0.686 19.609 21474 Z= 0.379 Chirality : 0.044 0.244 2432 Planarity : 0.004 0.053 1710 Dihedral : 29.874 169.045 4357 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.80 % Allowed : 18.75 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 are not related in a simple way. whole: 1.90 (0.26), residues: 1008 helix: 2.17 (0.21), residues: 644 sheet: 1.47 (1.02), residues: 27 loop : -0.59 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 979 TYR 0.070 0.002 TYR D 83 PHE 0.017 0.002 PHE M 938 TRP 0.015 0.002 TRP R 36 HIS 0.013 0.001 HIS A 996 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (14947) covalent geometry : angle 0.66133 / 0.38 (21465) hydrogen bonds : bond 0.04271 / 2.81 ( 844) hydrogen bonds : angle 3.16263 / 2.25 ( 2146) metal coordination : bond 0.00702 / 0.53 ( 14) metal coordination : angle 9.01241 / 5.09 ( 9) Misc. bond : bond 0.00118 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3842.30 seconds wall clock time: 66 minutes 9.27 seconds (3969.27 seconds total)