Starting phenix.real_space_refine on Wed Mar 4 15:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iej_35383/03_2026/8iej_35383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iej_35383/03_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_35383/03_2026/8iej_35383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iej_35383/03_2026/8iej_35383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/03_2026/8iej_35383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iej_35383/03_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-dev-5986/lib/python3.9/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: 3.24, per 1000 atoms: 0.23 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: 1.18 Conformation dependent library (CDL) restraints added in 485.3 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: 2.22 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: 2.74 Time building geometry restraints manager: 1.56 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=" CA ARG A 981 " pdb=" C ARG A 981 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.35e-02 5.49e+03 2.41e+00 bond pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CA CYS A 971 " pdb=" C CYS A 971 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.78e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.71e+00 ... (remaining 14942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 21333 2.62 - 5.25: 118 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=" N LYS A 955 " pdb=" CA LYS A 955 " pdb=" C LYS A 955 " ideal model delta sigma weight residual 110.28 115.76 -5.48 1.48e+00 4.57e-01 1.37e+01 angle pdb=" C GLU R 132 " pdb=" N ASN R 133 " pdb=" CA ASN R 133 " ideal model delta sigma weight residual 122.76 117.06 5.70 1.63e+00 3.76e-01 1.22e+01 angle pdb=" CB ARG R 11 " pdb=" CG ARG R 11 " pdb=" CD ARG R 11 " ideal model delta sigma weight residual 111.30 119.23 -7.93 2.30e+00 1.89e-01 1.19e+01 angle pdb=" N ARG M 928 " pdb=" CA ARG M 928 " pdb=" C ARG M 928 " ideal model delta sigma weight residual 108.34 112.71 -4.37 1.31e+00 5.83e-01 1.11e+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: 2140 0.059 - 0.119: 269 0.119 - 0.178: 21 0.178 - 0.237: 1 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=" 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 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.260 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.010 0.585 14963 Z= 0.488 Angle : 0.660 18.310 21474 Z= 0.383 Chirality : 0.040 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 covalent geometry : bond 0.00551 (14947) covalent geometry : angle 0.63806 (21465) hydrogen bonds : bond 0.09008 ( 844) hydrogen bonds : angle 3.88644 ( 2146) metal coordination : bond 0.24229 ( 14) metal coordination : angle 8.34178 ( 9) Misc. bond : bond 0.29501 ( 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 : 0.384 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: 0.1476 time to fit residues: 53.8031 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 : 0.334 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3685 r_free = 0.3685 target = 0.083249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050033 restraints weight = 47760.231| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.57 r_work: 0.2610 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- 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 = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14963 Z= 0.209 Angle : 0.630 21.290 21474 Z= 0.352 Chirality : 0.038 0.159 2432 Planarity : 0.005 0.073 1710 Dihedral : 29.457 169.632 4379 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.92 % Allowed : 9.50 % Favored : 88.58 % 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: 2.00 (0.27), residues: 1008 helix: 2.22 (0.21), residues: 644 sheet: -0.16 (0.81), residues: 39 loop : -0.29 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 981 TYR 0.022 0.002 TYR H 83 PHE 0.030 0.002 PHE R 13 TRP 0.011 0.001 TRP R 36 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00470 (14947) covalent geometry : angle 0.59795 (21465) hydrogen bonds : bond 0.04257 ( 844) hydrogen bonds : angle 3.20135 ( 2146) metal coordination : bond 0.01553 ( 14) metal coordination : angle 9.70509 ( 9) Misc. bond : bond 0.00114 ( 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 269 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 253 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9653 (mt) cc_final: 0.9405 (tt) REVERT: C 73 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8715 (t0) REVERT: C 90 ASP cc_start: 0.8892 (t70) cc_final: 0.8636 (t70) REVERT: D 68 ASP cc_start: 0.9400 (t70) cc_final: 0.9146 (t0) REVERT: E 59 GLU cc_start: 0.9132 (pm20) cc_final: 0.8892 (pm20) REVERT: G 13 LYS cc_start: 0.7346 (tptt) cc_final: 0.7130 (tppt) REVERT: G 36 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8677 (tmtt) REVERT: G 73 ASN cc_start: 0.8983 (OUTLIER) cc_final: 0.8751 (t0) REVERT: G 90 ASP cc_start: 0.8700 (t70) cc_final: 0.8351 (t0) REVERT: K 42 ARG cc_start: 0.8117 (mtp-110) cc_final: 0.7833 (ttt180) REVERT: K 56 LYS cc_start: 0.9386 (ttmm) cc_final: 0.9155 (ttpp) REVERT: K 59 GLU cc_start: 0.8890 (pm20) cc_final: 0.8459 (pm20) REVERT: A 962 LYS cc_start: 0.8575 (mtmt) cc_final: 0.8333 (mtmm) REVERT: M 938 PHE cc_start: 0.9197 (m-80) cc_final: 0.8519 (m-80) REVERT: M 951 ASP cc_start: 0.9255 (m-30) cc_final: 0.8771 (p0) REVERT: M 967 ASN cc_start: 0.9301 (m-40) cc_final: 0.8813 (m-40) outliers start: 16 outliers final: 7 residues processed: 258 average time/residue: 0.1487 time to fit residues: 52.5153 Evaluate side-chains 244 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN 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 L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.082029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.048890 restraints weight = 47905.379| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.59 r_work: 0.2572 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14963 Z= 0.281 Angle : 0.656 19.305 21474 Z= 0.368 Chirality : 0.040 0.167 2432 Planarity : 0.005 0.055 1710 Dihedral : 29.520 169.186 4365 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.68 % Allowed : 12.38 % Favored : 85.94 % 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: 1.87 (0.27), residues: 1008 helix: 2.16 (0.20), residues: 644 sheet: -0.92 (0.71), residues: 54 loop : -0.28 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 979 TYR 0.028 0.002 TYR D 83 PHE 0.016 0.002 PHE R 59 TRP 0.014 0.002 TRP R 36 HIS 0.011 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00637 (14947) covalent geometry : angle 0.62732 (21465) hydrogen bonds : bond 0.04713 ( 844) hydrogen bonds : angle 3.23062 ( 2146) metal coordination : bond 0.01436 ( 14) metal coordination : angle 9.35109 ( 9) Misc. bond : bond 0.00150 ( 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 258 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 244 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9667 (mt) cc_final: 0.9439 (tt) REVERT: C 73 ASN cc_start: 0.9077 (t0) cc_final: 0.8780 (t0) REVERT: C 90 ASP cc_start: 0.8919 (t70) cc_final: 0.8649 (t70) REVERT: C 92 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8341 (mt-10) REVERT: D 68 ASP cc_start: 0.9406 (t70) cc_final: 0.9185 (t0) REVERT: E 59 GLU cc_start: 0.9144 (pm20) cc_final: 0.8862 (pm20) REVERT: G 90 ASP cc_start: 0.8668 (t70) cc_final: 0.8321 (t0) REVERT: K 56 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9161 (ttpp) REVERT: K 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8439 (pm20) REVERT: A 962 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8370 (mtmm) REVERT: M 926 ASN cc_start: 0.9156 (m110) cc_final: 0.8854 (m110) REVERT: M 938 PHE cc_start: 0.9252 (m-80) cc_final: 0.8690 (m-80) REVERT: M 951 ASP cc_start: 0.9248 (m-30) cc_final: 0.8802 (p0) REVERT: M 967 ASN cc_start: 0.9232 (m-40) cc_final: 0.8751 (m-40) REVERT: R 80 ASN cc_start: 0.8265 (t0) cc_final: 0.7365 (t0) outliers start: 14 outliers final: 9 residues processed: 252 average time/residue: 0.1476 time to fit residues: 50.8839 Evaluate side-chains 239 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 946 VAL Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 125 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN L 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.083653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050609 restraints weight = 48032.069| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.58 r_work: 0.2628 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14963 Z= 0.164 Angle : 0.592 14.328 21474 Z= 0.338 Chirality : 0.036 0.158 2432 Planarity : 0.004 0.048 1710 Dihedral : 29.380 168.135 4357 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.56 % Allowed : 13.34 % 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: 2.07 (0.27), residues: 1008 helix: 2.34 (0.20), residues: 644 sheet: -0.55 (0.74), residues: 54 loop : -0.35 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 979 TYR 0.032 0.002 TYR H 83 PHE 0.015 0.001 PHE M 938 TRP 0.013 0.002 TRP R 36 HIS 0.014 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00364 (14947) covalent geometry : angle 0.56829 (21465) hydrogen bonds : bond 0.03793 ( 844) hydrogen bonds : angle 2.94907 ( 2146) metal coordination : bond 0.00723 ( 14) metal coordination : angle 8.16269 ( 9) Misc. bond : bond 0.00108 ( 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 273 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9639 (mt) cc_final: 0.9418 (tt) REVERT: C 73 ASN cc_start: 0.9121 (t0) cc_final: 0.8642 (t0) REVERT: C 90 ASP cc_start: 0.8922 (t70) cc_final: 0.8599 (t70) REVERT: D 68 ASP cc_start: 0.9390 (t70) cc_final: 0.9135 (t0) REVERT: E 59 GLU cc_start: 0.9150 (pm20) cc_final: 0.8888 (pm20) REVERT: F 88 TYR cc_start: 0.9341 (m-10) cc_final: 0.8947 (m-10) REVERT: G 73 ASN cc_start: 0.8880 (t160) cc_final: 0.8486 (t0) REVERT: G 90 ASP cc_start: 0.8662 (t70) cc_final: 0.8268 (t0) REVERT: K 56 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9124 (ttpp) REVERT: K 59 GLU cc_start: 0.8874 (pm20) cc_final: 0.8423 (pm20) REVERT: A 962 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8479 (mtmm) REVERT: A 969 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: A 996 HIS cc_start: 0.6905 (t-170) cc_final: 0.6619 (t-170) REVERT: M 926 ASN cc_start: 0.9133 (m110) cc_final: 0.8779 (m110) REVERT: M 938 PHE cc_start: 0.9247 (m-80) cc_final: 0.8708 (m-80) REVERT: M 951 ASP cc_start: 0.9211 (m-30) cc_final: 0.8732 (p0) REVERT: M 967 ASN cc_start: 0.9220 (m-40) cc_final: 0.8837 (m-40) REVERT: M 968 ASP cc_start: 0.9267 (m-30) cc_final: 0.8242 (t0) outliers start: 13 outliers final: 9 residues processed: 269 average time/residue: 0.1398 time to fit residues: 52.2231 Evaluate side-chains 255 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 245 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 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 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: 2.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 68 GLN R 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.049695 restraints weight = 48124.903| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.59 r_work: 0.2603 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14963 Z= 0.209 Angle : 0.615 13.335 21474 Z= 0.350 Chirality : 0.037 0.156 2432 Planarity : 0.004 0.073 1710 Dihedral : 29.440 168.119 4357 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.16 % Allowed : 15.26 % Favored : 82.57 % 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: 2.10 (0.27), residues: 1008 helix: 2.34 (0.21), residues: 646 sheet: -0.31 (0.76), residues: 54 loop : -0.32 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 979 TYR 0.056 0.002 TYR H 83 PHE 0.015 0.001 PHE M 938 TRP 0.010 0.002 TRP R 36 HIS 0.006 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00471 (14947) covalent geometry : angle 0.59520 (21465) hydrogen bonds : bond 0.04229 ( 844) hydrogen bonds : angle 3.00293 ( 2146) metal coordination : bond 0.00799 ( 14) metal coordination : angle 7.56457 ( 9) Misc. bond : bond 0.00325 ( 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 266 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9656 (mt) cc_final: 0.9427 (tt) REVERT: C 73 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8851 (t0) REVERT: C 90 ASP cc_start: 0.8944 (t70) cc_final: 0.8602 (t70) REVERT: C 92 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8702 (mm-30) REVERT: D 68 ASP cc_start: 0.9403 (t70) cc_final: 0.9163 (t0) REVERT: E 59 GLU cc_start: 0.9124 (pm20) cc_final: 0.8831 (pm20) REVERT: F 88 TYR cc_start: 0.9305 (m-10) cc_final: 0.9101 (m-10) REVERT: G 73 ASN cc_start: 0.8895 (t160) cc_final: 0.8612 (t0) REVERT: G 90 ASP cc_start: 0.8664 (t70) cc_final: 0.8129 (t0) REVERT: K 42 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7856 (ttt90) REVERT: K 56 LYS cc_start: 0.9412 (ttmm) cc_final: 0.9158 (ttpp) REVERT: K 59 GLU cc_start: 0.8870 (pm20) cc_final: 0.8422 (pm20) REVERT: K 120 MET cc_start: 0.9165 (mtt) cc_final: 0.8949 (mtt) REVERT: A 969 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.7850 (m-80) REVERT: A 996 HIS cc_start: 0.7022 (t-170) cc_final: 0.6815 (t-170) REVERT: M 938 PHE cc_start: 0.9234 (m-80) cc_final: 0.8592 (m-80) REVERT: M 951 ASP cc_start: 0.9248 (m-30) cc_final: 0.8730 (p0) REVERT: M 967 ASN cc_start: 0.9245 (m-40) cc_final: 0.8842 (m-40) REVERT: M 968 ASP cc_start: 0.9335 (m-30) cc_final: 0.8335 (t0) REVERT: R 12 ASP cc_start: 0.8343 (m-30) cc_final: 0.8104 (m-30) outliers start: 18 outliers final: 12 residues processed: 257 average time/residue: 0.1449 time to fit residues: 51.4616 Evaluate side-chains 253 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.083340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050641 restraints weight = 47419.080| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.65 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 = 0.34 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14963 Z= 0.175 Angle : 0.611 18.563 21474 Z= 0.343 Chirality : 0.036 0.166 2432 Planarity : 0.004 0.038 1710 Dihedral : 29.396 167.498 4357 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.56 % Allowed : 16.23 % Favored : 82.21 % 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: 2.18 (0.27), residues: 1008 helix: 2.41 (0.21), residues: 644 sheet: -0.17 (0.80), residues: 52 loop : -0.34 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 979 TYR 0.049 0.002 TYR D 83 PHE 0.020 0.001 PHE R 13 TRP 0.026 0.003 TRP R 36 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00391 (14947) covalent geometry : angle 0.58179 (21465) hydrogen bonds : bond 0.03866 ( 844) hydrogen bonds : angle 2.94518 ( 2146) metal coordination : bond 0.00747 ( 14) metal coordination : angle 9.18654 ( 9) Misc. bond : bond 0.00098 ( 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 265 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 252 time to evaluate : 0.405 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: 0.9053 (t0) cc_final: 0.8747 (t0) REVERT: C 90 ASP cc_start: 0.8917 (t70) cc_final: 0.8522 (t70) REVERT: D 68 ASP cc_start: 0.9393 (t70) cc_final: 0.9149 (t0) REVERT: E 59 GLU cc_start: 0.9127 (pm20) cc_final: 0.8852 (pm20) REVERT: G 73 ASN cc_start: 0.8925 (t160) cc_final: 0.8627 (t0) REVERT: G 74 LYS cc_start: 0.9593 (mtmm) cc_final: 0.9378 (ttmm) REVERT: G 90 ASP cc_start: 0.8667 (t70) cc_final: 0.8146 (t0) REVERT: H 93 GLU cc_start: 0.8878 (mp0) cc_final: 0.8622 (mp0) REVERT: K 56 LYS cc_start: 0.9400 (ttmm) cc_final: 0.9153 (ttpp) REVERT: K 59 GLU cc_start: 0.8887 (pm20) cc_final: 0.8448 (pm20) REVERT: K 120 MET cc_start: 0.9096 (mtt) cc_final: 0.8825 (mtm) REVERT: A 969 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: M 938 PHE cc_start: 0.9214 (m-80) cc_final: 0.8507 (m-80) REVERT: M 951 ASP cc_start: 0.9205 (m-30) cc_final: 0.8711 (p0) REVERT: M 967 ASN cc_start: 0.9220 (m-40) cc_final: 0.8822 (m-40) REVERT: M 968 ASP cc_start: 0.9300 (m-30) cc_final: 0.8345 (t0) REVERT: R 12 ASP cc_start: 0.8390 (m-30) cc_final: 0.8174 (m-30) outliers start: 13 outliers final: 11 residues processed: 259 average time/residue: 0.1461 time to fit residues: 52.1833 Evaluate side-chains 256 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 244 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 57 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3671 r_free = 0.3671 target = 0.082725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.049567 restraints weight = 47598.777| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.64 r_work: 0.2597 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.040 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14963 Z= 0.231 Angle : 0.635 16.990 21474 Z= 0.357 Chirality : 0.038 0.172 2432 Planarity : 0.004 0.045 1710 Dihedral : 29.473 167.313 4357 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.68 % Allowed : 17.55 % 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: 2.05 (0.27), residues: 1008 helix: 2.30 (0.21), residues: 646 sheet: -0.38 (0.92), residues: 42 loop : -0.34 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 981 TYR 0.069 0.002 TYR H 83 PHE 0.017 0.002 PHE R 13 TRP 0.030 0.004 TRP R 36 HIS 0.023 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00521 (14947) covalent geometry : angle 0.60953 (21465) hydrogen bonds : bond 0.04356 ( 844) hydrogen bonds : angle 3.06911 ( 2146) metal coordination : bond 0.00798 ( 14) metal coordination : angle 8.70965 ( 9) Misc. bond : bond 0.00083 ( 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 254 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.334 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: C 62 ILE cc_start: 0.9647 (mt) cc_final: 0.9423 (tt) REVERT: C 73 ASN cc_start: 0.9190 (t0) cc_final: 0.8863 (t0) REVERT: C 90 ASP cc_start: 0.8951 (t70) cc_final: 0.8652 (t0) REVERT: D 68 ASP cc_start: 0.9406 (t70) cc_final: 0.9175 (t0) REVERT: E 59 GLU cc_start: 0.9162 (pm20) cc_final: 0.8857 (pm20) REVERT: F 88 TYR cc_start: 0.9299 (m-10) cc_final: 0.8981 (m-10) REVERT: G 56 GLU cc_start: 0.9128 (tp30) cc_final: 0.8756 (tp30) REVERT: G 73 ASN cc_start: 0.9057 (t0) cc_final: 0.8740 (t0) REVERT: G 90 ASP cc_start: 0.8672 (t70) cc_final: 0.8130 (t0) REVERT: H 83 TYR cc_start: 0.7506 (m-80) cc_final: 0.7115 (m-80) REVERT: K 42 ARG cc_start: 0.8229 (mtp85) cc_final: 0.7938 (ttt180) REVERT: K 56 LYS cc_start: 0.9418 (ttmm) cc_final: 0.9164 (ttpp) REVERT: K 59 GLU cc_start: 0.8887 (pm20) cc_final: 0.8422 (pm20) REVERT: K 120 MET cc_start: 0.9124 (mtt) cc_final: 0.8845 (mtm) REVERT: A 969 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: M 938 PHE cc_start: 0.9220 (m-80) cc_final: 0.8724 (m-80) REVERT: M 951 ASP cc_start: 0.9232 (m-30) cc_final: 0.8778 (p0) REVERT: M 967 ASN cc_start: 0.9260 (m-40) cc_final: 0.8957 (m-40) REVERT: R 36 TRP cc_start: 0.7431 (m100) cc_final: 0.7186 (m100) outliers start: 14 outliers final: 10 residues processed: 248 average time/residue: 0.1479 time to fit residues: 50.5277 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 : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 983 CYS Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.084252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051607 restraints weight = 47605.260| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.59 r_work: 0.2659 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14963 Z= 0.153 Angle : 0.609 17.075 21474 Z= 0.342 Chirality : 0.036 0.183 2432 Planarity : 0.004 0.040 1710 Dihedral : 29.288 166.600 4356 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.44 % Allowed : 17.91 % 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: 2.13 (0.27), residues: 1008 helix: 2.39 (0.20), residues: 644 sheet: -0.28 (0.80), residues: 52 loop : -0.36 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 928 TYR 0.053 0.002 TYR H 83 PHE 0.015 0.001 PHE R 13 TRP 0.021 0.003 TRP R 36 HIS 0.018 0.001 HIS A 996 Details of bonding type rmsd covalent geometry : bond 0.00337 (14947) covalent geometry : angle 0.58276 (21465) hydrogen bonds : bond 0.03701 ( 844) hydrogen bonds : angle 2.91011 ( 2146) metal coordination : bond 0.00860 ( 14) metal coordination : angle 8.68035 ( 9) Misc. bond : bond 0.00034 ( 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 267 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 255 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9650 (mt) cc_final: 0.9423 (tt) REVERT: C 73 ASN cc_start: 0.9151 (t0) cc_final: 0.8801 (t0) REVERT: C 90 ASP cc_start: 0.8953 (t70) cc_final: 0.8554 (t70) REVERT: C 92 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8507 (mm-30) REVERT: D 68 ASP cc_start: 0.9409 (t70) cc_final: 0.9155 (t0) REVERT: E 59 GLU cc_start: 0.9156 (pm20) cc_final: 0.8886 (pm20) REVERT: G 56 GLU cc_start: 0.9109 (tp30) cc_final: 0.8824 (tp30) REVERT: G 73 ASN cc_start: 0.9035 (t0) cc_final: 0.8724 (t0) REVERT: G 74 LYS cc_start: 0.9615 (mtmm) cc_final: 0.9408 (ttmm) REVERT: G 90 ASP cc_start: 0.8614 (t70) cc_final: 0.8053 (t0) REVERT: H 93 GLU cc_start: 0.8892 (mp0) cc_final: 0.8671 (mp0) REVERT: K 42 ARG cc_start: 0.8200 (mtp85) cc_final: 0.7869 (ttt180) REVERT: K 56 LYS cc_start: 0.9379 (ttmm) cc_final: 0.9135 (ttpp) REVERT: K 59 GLU cc_start: 0.8864 (pm20) cc_final: 0.8460 (pm20) REVERT: K 120 MET cc_start: 0.9007 (mtt) cc_final: 0.8660 (mtm) REVERT: A 969 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: A 987 ASN cc_start: 0.9117 (m-40) cc_final: 0.8797 (t0) REVERT: M 936 LYS cc_start: 0.9057 (tptt) cc_final: 0.8679 (tppt) REVERT: M 938 PHE cc_start: 0.9185 (m-80) cc_final: 0.8761 (m-80) REVERT: M 951 ASP cc_start: 0.9181 (m-30) cc_final: 0.8732 (p0) REVERT: M 967 ASN cc_start: 0.9191 (m-40) cc_final: 0.8935 (m-40) REVERT: R 36 TRP cc_start: 0.7317 (m100) cc_final: 0.6849 (m100) REVERT: R 101 ASP cc_start: 0.8401 (p0) cc_final: 0.7917 (m-30) outliers start: 12 outliers final: 8 residues processed: 262 average time/residue: 0.1450 time to fit residues: 52.5531 Evaluate side-chains 253 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE 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: 5.9990 chunk 120 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.081882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.048501 restraints weight = 48000.204| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.65 r_work: 0.2567 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14963 Z= 0.296 Angle : 0.697 25.289 21474 Z= 0.384 Chirality : 0.041 0.193 2432 Planarity : 0.005 0.046 1710 Dihedral : 29.626 166.890 4356 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 18.03 % Favored : 80.17 % 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: 1.90 (0.27), residues: 1008 helix: 2.18 (0.21), residues: 646 sheet: -0.91 (0.84), residues: 43 loop : -0.33 (0.33), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 981 TYR 0.074 0.003 TYR H 83 PHE 0.015 0.002 PHE R 13 TRP 0.018 0.003 TRP R 36 HIS 0.021 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00674 (14947) covalent geometry : angle 0.66236 (21465) hydrogen bonds : bond 0.04956 ( 844) hydrogen bonds : angle 3.25507 ( 2146) metal coordination : bond 0.01073 ( 14) metal coordination : angle 10.65664 ( 9) Misc. bond : bond 0.00080 ( 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 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.493 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: C 62 ILE cc_start: 0.9647 (mt) cc_final: 0.9423 (tt) REVERT: C 73 ASN cc_start: 0.9247 (t0) cc_final: 0.8860 (t0) REVERT: C 90 ASP cc_start: 0.9049 (t70) cc_final: 0.8737 (t0) REVERT: D 68 ASP cc_start: 0.9417 (t70) cc_final: 0.9200 (t0) REVERT: E 59 GLU cc_start: 0.9152 (pm20) cc_final: 0.8813 (pm20) REVERT: G 56 GLU cc_start: 0.9135 (tp30) cc_final: 0.8801 (tp30) REVERT: G 73 ASN cc_start: 0.9156 (t0) cc_final: 0.8773 (t0) REVERT: G 90 ASP cc_start: 0.8695 (t70) cc_final: 0.8343 (t0) REVERT: K 56 LYS cc_start: 0.9427 (ttmm) cc_final: 0.9169 (ttpp) REVERT: K 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8393 (pm20) REVERT: K 120 MET cc_start: 0.9150 (mtt) cc_final: 0.8873 (mtm) REVERT: A 969 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: A 987 ASN cc_start: 0.9276 (m-40) cc_final: 0.8939 (t0) REVERT: A 996 HIS cc_start: 0.6545 (t-170) cc_final: 0.6088 (t-170) REVERT: M 936 LYS cc_start: 0.9050 (tptt) cc_final: 0.8726 (tppt) REVERT: M 938 PHE cc_start: 0.9224 (m-80) cc_final: 0.8665 (m-80) REVERT: M 951 ASP cc_start: 0.9225 (m-30) cc_final: 0.8800 (p0) REVERT: M 968 ASP cc_start: 0.9404 (m-30) cc_final: 0.9026 (m-30) REVERT: R 36 TRP cc_start: 0.7568 (m100) cc_final: 0.7076 (m100) REVERT: R 53 PHE cc_start: 0.6760 (m-80) cc_final: 0.6261 (m-80) outliers start: 15 outliers final: 9 residues processed: 245 average time/residue: 0.1466 time to fit residues: 49.6398 Evaluate side-chains 237 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 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 979 ARG Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE 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: 0.8980 chunk 54 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 15 optimal weight: 0.0030 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.084326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051701 restraints weight = 47875.851| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.60 r_work: 0.2659 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2574 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= 0.154 Angle : 0.652 24.620 21474 Z= 0.361 Chirality : 0.037 0.190 2432 Planarity : 0.004 0.047 1710 Dihedral : 29.337 165.724 4355 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.08 % Allowed : 19.47 % 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: 1.89 (0.26), residues: 1008 helix: 2.21 (0.20), residues: 644 sheet: -0.80 (0.84), residues: 43 loop : -0.41 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 928 TYR 0.060 0.002 TYR H 83 PHE 0.016 0.001 PHE R 13 TRP 0.019 0.002 TRP R 36 HIS 0.019 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00335 (14947) covalent geometry : angle 0.61877 (21465) hydrogen bonds : bond 0.03834 ( 844) hydrogen bonds : angle 3.01212 ( 2146) metal coordination : bond 0.01111 ( 14) metal coordination : angle 10.12723 ( 9) Misc. bond : bond 0.00049 ( 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 253 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 244 time to evaluate : 0.397 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: C 62 ILE cc_start: 0.9648 (mt) cc_final: 0.9421 (tt) REVERT: C 73 ASN cc_start: 0.9153 (t0) cc_final: 0.8608 (t0) REVERT: C 90 ASP cc_start: 0.8995 (t70) cc_final: 0.8588 (t70) REVERT: D 68 ASP cc_start: 0.9413 (t70) cc_final: 0.9166 (t0) REVERT: E 59 GLU cc_start: 0.9147 (pm20) cc_final: 0.8869 (pm20) REVERT: G 56 GLU cc_start: 0.9087 (tp30) cc_final: 0.8810 (tp30) REVERT: G 73 ASN cc_start: 0.9114 (t0) cc_final: 0.8760 (t0) REVERT: G 90 ASP cc_start: 0.8637 (t70) cc_final: 0.8081 (t0) REVERT: H 46 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9091 (mmmt) REVERT: H 68 ASP cc_start: 0.9351 (t0) cc_final: 0.9097 (t0) REVERT: K 42 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7873 (ttt90) REVERT: K 56 LYS cc_start: 0.9349 (ttmm) cc_final: 0.9112 (ttpp) REVERT: K 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8448 (pm20) REVERT: K 120 MET cc_start: 0.9002 (mtt) cc_final: 0.8665 (mtm) REVERT: A 969 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 987 ASN cc_start: 0.9169 (m-40) cc_final: 0.8949 (t0) REVERT: A 996 HIS cc_start: 0.6674 (t-170) cc_final: 0.6350 (t-170) REVERT: M 936 LYS cc_start: 0.9056 (tptt) cc_final: 0.8648 (tppt) REVERT: M 938 PHE cc_start: 0.9119 (m-80) cc_final: 0.8677 (m-80) REVERT: M 951 ASP cc_start: 0.9157 (m-30) cc_final: 0.8657 (m-30) REVERT: R 36 TRP cc_start: 0.7433 (m100) cc_final: 0.6751 (m100) REVERT: R 53 PHE cc_start: 0.6773 (m-80) cc_final: 0.5951 (m-80) REVERT: R 76 MET cc_start: 0.2130 (mmt) cc_final: 0.0337 (ttm) REVERT: R 101 ASP cc_start: 0.8496 (p0) cc_final: 0.8091 (m-30) outliers start: 9 outliers final: 7 residues processed: 251 average time/residue: 0.1286 time to fit residues: 45.5536 Evaluate side-chains 249 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 50 ILE 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 A residue 990 PHE 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 95 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 122 optimal weight: 30.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN A 980 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.084009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051586 restraints weight = 47960.196| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.57 r_work: 0.2653 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2651 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2651 r_free = 0.2651 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2651 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14963 Z= 0.166 Angle : 0.642 24.248 21474 Z= 0.356 Chirality : 0.037 0.185 2432 Planarity : 0.004 0.038 1710 Dihedral : 29.339 166.481 4355 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.08 % Allowed : 19.83 % Favored : 79.09 % 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: 1.95 (0.26), residues: 1008 helix: 2.21 (0.20), residues: 646 sheet: 0.54 (1.01), residues: 28 loop : -0.47 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 79 TYR 0.067 0.002 TYR H 83 PHE 0.015 0.001 PHE R 13 TRP 0.018 0.002 TRP R 36 HIS 0.017 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (14947) covalent geometry : angle 0.60927 (21465) hydrogen bonds : bond 0.03895 ( 844) hydrogen bonds : angle 3.02838 ( 2146) metal coordination : bond 0.00934 ( 14) metal coordination : angle 9.94369 ( 9) Misc. bond : bond 0.00054 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4375.41 seconds wall clock time: 75 minutes 11.37 seconds (4511.37 seconds total)