Starting phenix.real_space_refine on Wed Aug 5 20:16:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.map" model { file = "/net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qaj_52975/08_2026/9qaj_52975.cif" } resolution = 2.95 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= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 12 5.16 5 C 6714 2.51 5 N 2285 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12144 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 700 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 83 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 2.41, per 1000 atoms: 0.20 Number of scatterers: 12144 At special positions: 0 Unit cell: (123.201, 98.415, 114.453, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 288 15.00 O 2845 8.00 N 2285 7.00 C 6714 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 284.7 milliseconds 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 75.5% alpha, 3.0% beta 141 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.899A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.548A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.752A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.435A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.755A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.528A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.509A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.461A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 3 through 10 removed outlier: 3.531A pdb=" N THR K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 26 removed outlier: 3.793A pdb=" N GLU L 26 " --> pdb=" O MET L 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.532A pdb=" N THR M 10 " --> pdb=" O VAL M 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 30 removed outlier: 3.824A pdb=" N VAL N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.708A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.144A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.949A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.970A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.477A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 436 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 720 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.13 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: 2690 1.33 - 1.45: 3999 1.45 - 1.57: 5655 1.57 - 1.69: 576 1.69 - 1.81: 22 Bond restraints: 12942 Sorted by residual: bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA I -53 " pdb=" C2' DA I -53 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 23 " pdb=" C2' DG I 23 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 bond pdb=" C3' DG I 20 " pdb=" C2' DG I 20 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.67e+00 ... (remaining 12937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 17224 1.42 - 2.83: 1409 2.83 - 4.25: 81 4.25 - 5.66: 11 5.66 - 7.08: 3 Bond angle restraints: 18728 Sorted by residual: angle pdb=" O4' DG J -49 " pdb=" C4' DG J -49 " pdb=" C3' DG J -49 " ideal model delta sigma weight residual 106.00 103.14 2.86 6.00e-01 2.78e+00 2.27e+01 angle pdb=" O4' DG I -35 " pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.24e+01 angle pdb=" O4' DG J 2 " pdb=" C4' DG J 2 " pdb=" C3' DG J 2 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J -16 " pdb=" C4 DT J -16 " pdb=" O4 DT J -16 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 ... (remaining 18723 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 5014 25.88 - 51.77: 1577 51.77 - 77.65: 440 77.65 - 103.54: 6 103.54 - 129.42: 1 Dihedral angle restraints: 7038 sinusoidal: 4732 harmonic: 2306 Sorted by residual: dihedral pdb=" C4' DC J -38 " pdb=" C3' DC J -38 " pdb=" O3' DC J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 90.58 129.42 1 3.50e+01 8.16e-04 1.28e+01 dihedral pdb=" CA ARG M 7 " pdb=" CB ARG M 7 " pdb=" CG ARG M 7 " pdb=" CD ARG M 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.40 59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG K 7 " pdb=" CB ARG K 7 " pdb=" CG ARG K 7 " pdb=" CD ARG K 7 " ideal model delta sinusoidal sigma weight residual -60.00 -119.38 59.38 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 7035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1225 0.030 - 0.060: 555 0.060 - 0.089: 220 0.089 - 0.119: 120 0.119 - 0.149: 21 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" C3' DA J -35 " pdb=" C4' DA J -35 " pdb=" O3' DA J -35 " pdb=" C2' DA J -35 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 5.19e-01 ... (remaining 2138 not shown) Planarity restraints: 1371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.023 2.00e-02 2.50e+03 9.23e-03 2.56e+00 pdb=" N9 DG I -35 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 17 " 0.020 2.00e-02 2.50e+03 9.30e-03 2.38e+00 pdb=" N9 DA J 17 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA J 17 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA J 17 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA J 17 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 17 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DA J 17 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA J 17 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 17 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA J 17 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -49 " -0.018 2.00e-02 2.50e+03 8.66e-03 2.25e+00 pdb=" N9 DG J -49 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DG J -49 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG J -49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG J -49 " -0.006 2.00e-02 2.50e+03 pdb=" O6 DG J -49 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG J -49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG J -49 " -0.004 2.00e-02 2.50e+03 pdb=" N2 DG J -49 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG J -49 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG J -49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1368 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 590 2.70 - 3.25: 11214 3.25 - 3.80: 23934 3.80 - 4.35: 28428 4.35 - 4.90: 41259 Nonbonded interactions: 105425 Sorted by model distance: nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.149 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.164 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.165 3.040 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.190 3.120 nonbonded pdb=" OE1 GLU G 64 " pdb=" NH1 ARG M 7 " model vdw 2.196 3.120 ... (remaining 105420 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 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 36 through 124) selection = (chain 'H' and resid 36 through 124) } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.440 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12942 Z= 0.549 Angle : 0.752 7.078 18728 Z= 0.669 Chirality : 0.044 0.149 2141 Planarity : 0.003 0.030 1371 Dihedral : 28.272 129.423 5546 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.32 % Allowed : 19.24 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.31), residues: 772 helix: 2.75 (0.22), residues: 569 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 79 TYR 0.018 0.001 TYR G 50 PHE 0.016 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.55 (12942) covalent geometry : angle 0.75154 / 0.67 (18728) hydrogen bonds : bond 0.10853 / 7.44 ( 796) hydrogen bonds : angle 3.81554 / 2.90 ( 2004) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.321 Fit side-chains REVERT: B 59 LYS cc_start: 0.9159 (tttm) cc_final: 0.8804 (tppp) REVERT: B 63 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 92 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8448 (mm-30) REVERT: H 46 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8669 (mmmt) REVERT: H 71 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7976 (mm-30) outliers start: 2 outliers final: 5 residues processed: 224 average time/residue: 0.6291 time to fit residues: 150.9967 Evaluate side-chains 213 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain E residue 74 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.1980 chunk 100 optimal weight: 40.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN C 112 GLN F 93 GLN G 94 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.036292 restraints weight = 44507.623| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.86 r_work: 0.2395 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9093 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12942 Z= 0.183 Angle : 0.647 6.054 18728 Z= 0.382 Chirality : 0.044 0.200 2141 Planarity : 0.004 0.040 1371 Dihedral : 31.091 127.319 4061 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.37 % Allowed : 24.29 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.54 (0.31), residues: 772 helix: 2.63 (0.22), residues: 585 sheet: None (None), residues: 0 loop : -1.58 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.016 0.001 TYR G 57 PHE 0.014 0.002 PHE F 100 HIS 0.004 0.001 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.18 (12942) covalent geometry : angle 0.64664 / 0.38 (18728) hydrogen bonds : bond 0.04778 / 3.25 ( 796) hydrogen bonds : angle 3.33084 / 2.49 ( 2004) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.241 Fit side-chains REVERT: B 59 LYS cc_start: 0.9287 (tttm) cc_final: 0.8968 (tppp) REVERT: B 63 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8976 (mt-10) REVERT: C 90 ASP cc_start: 0.8541 (t0) cc_final: 0.8069 (t0) REVERT: C 92 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8810 (mt-10) REVERT: D 68 ASP cc_start: 0.9467 (t0) cc_final: 0.9233 (t0) REVERT: D 105 GLU cc_start: 0.8692 (tp30) cc_final: 0.8237 (tp30) REVERT: E 59 GLU cc_start: 0.8986 (pm20) cc_final: 0.8767 (pm20) REVERT: G 39 TYR cc_start: 0.9307 (m-80) cc_final: 0.9049 (m-80) REVERT: G 41 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8367 (tm-30) REVERT: H 46 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8929 (mmmt) REVERT: H 68 ASP cc_start: 0.9493 (t0) cc_final: 0.9251 (t0) REVERT: H 71 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9079 (mm-30) REVERT: H 105 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8326 (tm-30) outliers start: 15 outliers final: 8 residues processed: 233 average time/residue: 0.6299 time to fit residues: 157.6103 Evaluate side-chains 217 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 77 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN G 94 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.037126 restraints weight = 44356.242| |-----------------------------------------------------------------------------| r_work (start): 0.2633 rms_B_bonded: 2.86 r_work: 0.2431 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12942 Z= 0.144 Angle : 0.608 7.225 18728 Z= 0.362 Chirality : 0.041 0.189 2141 Planarity : 0.004 0.037 1371 Dihedral : 31.096 127.738 4055 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.52 % Allowed : 25.39 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.30), residues: 772 helix: 2.67 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 7 TYR 0.020 0.001 TYR G 50 PHE 0.010 0.001 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (12942) covalent geometry : angle 0.60826 / 0.36 (18728) hydrogen bonds : bond 0.04094 / 2.77 ( 796) hydrogen bonds : angle 3.03023 / 2.27 ( 2004) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.288 Fit side-chains REVERT: B 59 LYS cc_start: 0.9270 (tttm) cc_final: 0.8901 (tppp) REVERT: B 63 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8861 (mt-10) REVERT: C 64 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8794 (tm-30) REVERT: C 90 ASP cc_start: 0.8538 (t0) cc_final: 0.8115 (t0) REVERT: C 92 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8763 (mt-10) REVERT: D 68 ASP cc_start: 0.9423 (t0) cc_final: 0.9151 (t0) REVERT: D 86 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8447 (tpp80) REVERT: D 93 GLU cc_start: 0.9050 (mp0) cc_final: 0.8770 (mm-30) REVERT: E 59 GLU cc_start: 0.8940 (pm20) cc_final: 0.8643 (pm20) REVERT: G 39 TYR cc_start: 0.9322 (m-80) cc_final: 0.9023 (m-80) REVERT: G 41 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8207 (tm-30) REVERT: G 90 ASP cc_start: 0.8817 (t0) cc_final: 0.8602 (t0) REVERT: H 46 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8950 (mmmt) REVERT: H 68 ASP cc_start: 0.9523 (t0) cc_final: 0.9243 (t0) REVERT: H 71 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9039 (mm-30) REVERT: H 105 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8227 (tm-30) outliers start: 16 outliers final: 8 residues processed: 235 average time/residue: 0.5843 time to fit residues: 147.6746 Evaluate side-chains 222 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 213 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 89 optimal weight: 30.0000 chunk 42 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 97 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 57 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN E 113 HIS G 94 ASN H 47 GLN H 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.057036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.036619 restraints weight = 44738.400| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 2.86 r_work: 0.2409 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12942 Z= 0.192 Angle : 0.630 6.159 18728 Z= 0.367 Chirality : 0.042 0.196 2141 Planarity : 0.004 0.037 1371 Dihedral : 31.145 127.634 4055 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.79 % Allowed : 26.81 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.70 (0.31), residues: 772 helix: 2.78 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.64 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 99 TYR 0.020 0.002 TYR B 88 PHE 0.014 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (12942) covalent geometry : angle 0.62958 / 0.37 (18728) hydrogen bonds : bond 0.04272 / 2.90 ( 796) hydrogen bonds : angle 3.07439 / 2.29 ( 2004) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 0.206 Fit side-chains REVERT: B 59 LYS cc_start: 0.9297 (tttm) cc_final: 0.8994 (tppp) REVERT: B 63 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8960 (mt-10) REVERT: C 64 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8752 (tm-30) REVERT: C 90 ASP cc_start: 0.8613 (t0) cc_final: 0.8107 (t0) REVERT: C 92 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8708 (mt-10) REVERT: D 68 ASP cc_start: 0.9434 (t0) cc_final: 0.9145 (t0) REVERT: D 86 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8465 (tpp80) REVERT: D 93 GLU cc_start: 0.9143 (mp0) cc_final: 0.8920 (mp0) REVERT: D 105 GLU cc_start: 0.8627 (tp30) cc_final: 0.8121 (tp30) REVERT: E 59 GLU cc_start: 0.8911 (pm20) cc_final: 0.8611 (pm20) REVERT: G 41 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8179 (tm-30) REVERT: G 64 GLU cc_start: 0.9425 (tt0) cc_final: 0.9009 (tm-30) REVERT: G 90 ASP cc_start: 0.8834 (t0) cc_final: 0.8554 (t0) REVERT: H 46 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8936 (mmmt) REVERT: H 68 ASP cc_start: 0.9542 (t0) cc_final: 0.9250 (t0) REVERT: H 71 GLU cc_start: 0.9311 (mm-30) cc_final: 0.9094 (mm-30) REVERT: H 105 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8308 (tm-30) outliers start: 24 outliers final: 14 residues processed: 225 average time/residue: 0.5287 time to fit residues: 128.0848 Evaluate side-chains 223 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 14 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.036381 restraints weight = 44977.570| |-----------------------------------------------------------------------------| r_work (start): 0.2603 rms_B_bonded: 2.88 r_work: 0.2400 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12942 Z= 0.202 Angle : 0.638 6.175 18728 Z= 0.368 Chirality : 0.042 0.199 2141 Planarity : 0.004 0.048 1371 Dihedral : 31.196 127.762 4055 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.79 % Allowed : 27.29 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.31), residues: 772 helix: 2.84 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.57 (0.40), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 35 TYR 0.021 0.002 TYR G 50 PHE 0.014 0.002 PHE F 100 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (12942) covalent geometry : angle 0.63785 / 0.37 (18728) hydrogen bonds : bond 0.04278 / 2.91 ( 796) hydrogen bonds : angle 3.04399 / 2.27 ( 2004) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.212 Fit side-chains REVERT: B 59 LYS cc_start: 0.9310 (tttm) cc_final: 0.8909 (tppp) REVERT: B 63 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8804 (mt-10) REVERT: C 64 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8785 (tm-30) REVERT: C 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8066 (t0) REVERT: C 92 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: D 68 ASP cc_start: 0.9431 (t0) cc_final: 0.9159 (t0) REVERT: D 86 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8502 (tpp80) REVERT: D 93 GLU cc_start: 0.9183 (mp0) cc_final: 0.8940 (mp0) REVERT: E 59 GLU cc_start: 0.8947 (pm20) cc_final: 0.8643 (pm20) REVERT: G 41 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8146 (tm-30) REVERT: G 64 GLU cc_start: 0.9413 (tt0) cc_final: 0.9048 (tm-30) REVERT: G 90 ASP cc_start: 0.8908 (t0) cc_final: 0.8641 (t0) REVERT: H 46 LYS cc_start: 0.9185 (mmmt) cc_final: 0.8901 (mmmt) REVERT: H 68 ASP cc_start: 0.9548 (t0) cc_final: 0.9247 (t0) REVERT: H 71 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9110 (mm-30) REVERT: H 105 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8271 (tm-30) outliers start: 24 outliers final: 14 residues processed: 218 average time/residue: 0.5596 time to fit residues: 131.0905 Evaluate side-chains 220 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 74 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 7 optimal weight: 4.9990 chunk 97 optimal weight: 50.0000 chunk 22 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN G 94 ASN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.037416 restraints weight = 44575.151| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.88 r_work: 0.2441 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12942 Z= 0.141 Angle : 0.602 6.660 18728 Z= 0.355 Chirality : 0.041 0.189 2141 Planarity : 0.004 0.044 1371 Dihedral : 31.083 127.770 4055 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.47 % Allowed : 27.13 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.83 (0.30), residues: 772 helix: 2.85 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.51 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.020 0.001 TYR G 50 PHE 0.011 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12942) covalent geometry : angle 0.60246 / 0.35 (18728) hydrogen bonds : bond 0.03783 / 2.55 ( 796) hydrogen bonds : angle 2.88319 / 2.15 ( 2004) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 233 time to evaluate : 0.333 Fit side-chains REVERT: A 76 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8814 (tm-30) REVERT: B 59 LYS cc_start: 0.9280 (tttm) cc_final: 0.8950 (tppp) REVERT: B 63 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8904 (mt-10) REVERT: C 64 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8726 (tm-30) REVERT: C 90 ASP cc_start: 0.8536 (t0) cc_final: 0.8176 (t0) REVERT: C 92 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: D 68 ASP cc_start: 0.9421 (t0) cc_final: 0.9183 (t0) REVERT: D 86 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.8466 (tpp80) REVERT: D 93 GLU cc_start: 0.9154 (mp0) cc_final: 0.8890 (mp0) REVERT: D 105 GLU cc_start: 0.8607 (tp30) cc_final: 0.8089 (tp30) REVERT: E 59 GLU cc_start: 0.8905 (pm20) cc_final: 0.8588 (pm20) REVERT: E 107 THR cc_start: 0.9736 (m) cc_final: 0.9499 (p) REVERT: G 41 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8252 (tm-30) REVERT: G 64 GLU cc_start: 0.9384 (OUTLIER) cc_final: 0.9032 (tm-30) REVERT: G 90 ASP cc_start: 0.8893 (t0) cc_final: 0.8593 (t0) REVERT: H 34 LYS cc_start: 0.8810 (mppt) cc_final: 0.8481 (mmpt) REVERT: H 46 LYS cc_start: 0.9156 (mmmt) cc_final: 0.8891 (mmmt) REVERT: H 68 ASP cc_start: 0.9531 (t0) cc_final: 0.9237 (t0) REVERT: H 71 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9096 (mm-30) REVERT: H 105 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8163 (tm-30) outliers start: 22 outliers final: 11 residues processed: 236 average time/residue: 0.5678 time to fit residues: 144.2318 Evaluate side-chains 231 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 216 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 87 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 47 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.058242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.037883 restraints weight = 44602.195| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.85 r_work: 0.2451 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12942 Z= 0.142 Angle : 0.612 6.200 18728 Z= 0.357 Chirality : 0.040 0.188 2141 Planarity : 0.004 0.041 1371 Dihedral : 31.072 127.683 4055 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.31 % Allowed : 29.02 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.30), residues: 772 helix: 2.88 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.48 (0.40), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.020 0.001 TYR G 50 PHE 0.010 0.001 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (12942) covalent geometry : angle 0.61167 / 0.36 (18728) hydrogen bonds : bond 0.03760 / 2.54 ( 796) hydrogen bonds : angle 2.86564 / 2.13 ( 2004) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 0.241 Fit side-chains REVERT: B 59 LYS cc_start: 0.9270 (tttm) cc_final: 0.9020 (tppp) REVERT: C 64 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8731 (tm-30) REVERT: C 90 ASP cc_start: 0.8644 (t0) cc_final: 0.8160 (t0) REVERT: C 92 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8635 (mt-10) REVERT: D 68 ASP cc_start: 0.9395 (t0) cc_final: 0.9161 (t0) REVERT: D 86 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8493 (tpp80) REVERT: D 93 GLU cc_start: 0.9154 (mp0) cc_final: 0.8860 (mp0) REVERT: E 59 GLU cc_start: 0.8884 (pm20) cc_final: 0.8574 (pm20) REVERT: E 107 THR cc_start: 0.9733 (m) cc_final: 0.9494 (p) REVERT: G 64 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9031 (tm-30) REVERT: G 90 ASP cc_start: 0.8890 (t0) cc_final: 0.8569 (t0) REVERT: H 46 LYS cc_start: 0.9143 (mmmt) cc_final: 0.8857 (mmmt) REVERT: H 68 ASP cc_start: 0.9521 (t0) cc_final: 0.9219 (t0) REVERT: H 71 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9092 (mm-30) REVERT: H 105 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8137 (tm-30) outliers start: 21 outliers final: 11 residues processed: 231 average time/residue: 0.5738 time to fit residues: 142.5815 Evaluate side-chains 232 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 218 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 60 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 23 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN G 94 ASN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.036736 restraints weight = 44841.205| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 2.86 r_work: 0.2419 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12942 Z= 0.202 Angle : 0.651 7.672 18728 Z= 0.370 Chirality : 0.042 0.196 2141 Planarity : 0.004 0.047 1371 Dihedral : 31.178 127.610 4055 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.68 % Allowed : 30.91 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.91 (0.31), residues: 772 helix: 2.90 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.49 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 79 TYR 0.020 0.002 TYR G 50 PHE 0.014 0.001 PHE F 100 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.20 (12942) covalent geometry : angle 0.65143 / 0.37 (18728) hydrogen bonds : bond 0.04199 / 2.86 ( 796) hydrogen bonds : angle 2.99687 / 2.22 ( 2004) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: C 56 GLU cc_start: 0.9227 (tp30) cc_final: 0.9022 (tp30) REVERT: C 64 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8765 (tm-30) REVERT: C 90 ASP cc_start: 0.8672 (t0) cc_final: 0.8067 (t0) REVERT: C 92 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: D 68 ASP cc_start: 0.9419 (t0) cc_final: 0.9179 (t0) REVERT: D 86 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.8511 (tpp80) REVERT: D 93 GLU cc_start: 0.9181 (mp0) cc_final: 0.8880 (mp0) REVERT: D 105 GLU cc_start: 0.8662 (tp30) cc_final: 0.8242 (tp30) REVERT: E 59 GLU cc_start: 0.8921 (pm20) cc_final: 0.8613 (pm20) REVERT: E 107 THR cc_start: 0.9742 (m) cc_final: 0.9477 (p) REVERT: G 64 GLU cc_start: 0.9405 (tt0) cc_final: 0.9068 (tm-30) REVERT: G 90 ASP cc_start: 0.8942 (t0) cc_final: 0.8638 (t0) REVERT: H 46 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8893 (mmmt) REVERT: H 68 ASP cc_start: 0.9536 (t0) cc_final: 0.9233 (t0) REVERT: H 71 GLU cc_start: 0.9318 (mm-30) cc_final: 0.9097 (mm-30) REVERT: H 105 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8229 (tm-30) outliers start: 17 outliers final: 13 residues processed: 219 average time/residue: 0.5670 time to fit residues: 133.3327 Evaluate side-chains 227 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 113 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 75 optimal weight: 30.0000 chunk 97 optimal weight: 50.0000 chunk 55 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.035739 restraints weight = 44698.516| |-----------------------------------------------------------------------------| r_work (start): 0.2587 rms_B_bonded: 2.86 r_work: 0.2383 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12942 Z= 0.260 Angle : 0.708 8.210 18728 Z= 0.393 Chirality : 0.044 0.205 2141 Planarity : 0.004 0.050 1371 Dihedral : 31.347 127.537 4055 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.84 % Allowed : 31.23 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.31), residues: 772 helix: 2.90 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.52 (0.42), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 79 TYR 0.025 0.002 TYR G 50 PHE 0.016 0.002 PHE F 100 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.26 (12942) covalent geometry : angle 0.70836 / 0.39 (18728) hydrogen bonds : bond 0.04684 / 3.21 ( 796) hydrogen bonds : angle 3.14386 / 2.32 ( 2004) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: C 64 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8913 (tm-30) REVERT: C 90 ASP cc_start: 0.8618 (t0) cc_final: 0.7976 (t0) REVERT: C 92 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8716 (mp0) REVERT: D 68 ASP cc_start: 0.9431 (t0) cc_final: 0.9186 (t0) REVERT: D 86 ARG cc_start: 0.9337 (OUTLIER) cc_final: 0.8493 (tpp80) REVERT: D 93 GLU cc_start: 0.9231 (mp0) cc_final: 0.8932 (mp0) REVERT: D 105 GLU cc_start: 0.8716 (tp30) cc_final: 0.7974 (tp30) REVERT: E 59 GLU cc_start: 0.8997 (pm20) cc_final: 0.8678 (pm20) REVERT: F 77 LYS cc_start: 0.9676 (OUTLIER) cc_final: 0.9474 (mtpt) REVERT: G 64 GLU cc_start: 0.9417 (tt0) cc_final: 0.9075 (tm-30) REVERT: G 90 ASP cc_start: 0.8945 (t0) cc_final: 0.8633 (t0) REVERT: H 34 LYS cc_start: 0.8779 (mppt) cc_final: 0.8501 (mmpt) REVERT: H 46 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8895 (mmmt) REVERT: H 68 ASP cc_start: 0.9551 (t0) cc_final: 0.9233 (t0) REVERT: H 71 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9114 (mm-30) REVERT: H 105 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8351 (tm-30) outliers start: 18 outliers final: 11 residues processed: 215 average time/residue: 0.5597 time to fit residues: 129.2243 Evaluate side-chains 216 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 118 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 18 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 97 optimal weight: 40.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN C 112 GLN G 94 ASN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.036727 restraints weight = 44900.541| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.89 r_work: 0.2418 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12942 Z= 0.152 Angle : 0.642 10.281 18728 Z= 0.366 Chirality : 0.041 0.193 2141 Planarity : 0.004 0.049 1371 Dihedral : 31.202 127.427 4055 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.89 % Allowed : 32.65 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.92 (0.31), residues: 772 helix: 2.91 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 79 TYR 0.024 0.002 TYR G 50 PHE 0.012 0.002 PHE F 100 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (12942) covalent geometry : angle 0.64217 / 0.37 (18728) hydrogen bonds : bond 0.03853 / 2.60 ( 796) hydrogen bonds : angle 2.97397 / 2.20 ( 2004) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1544 Ramachandran restraints generated. 772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9095 (pt0) cc_final: 0.8642 (pp30) REVERT: C 64 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8852 (tm-30) REVERT: C 92 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8661 (mt-10) REVERT: D 68 ASP cc_start: 0.9421 (t0) cc_final: 0.9185 (t0) REVERT: D 86 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8465 (tpp80) REVERT: D 93 GLU cc_start: 0.9188 (mp0) cc_final: 0.8880 (mp0) REVERT: D 105 GLU cc_start: 0.8614 (tp30) cc_final: 0.8149 (tp30) REVERT: E 59 GLU cc_start: 0.8958 (pm20) cc_final: 0.8637 (pm20) REVERT: G 64 GLU cc_start: 0.9381 (tt0) cc_final: 0.9046 (tm-30) REVERT: G 90 ASP cc_start: 0.8958 (t0) cc_final: 0.8639 (t0) REVERT: H 34 LYS cc_start: 0.8778 (mppt) cc_final: 0.8479 (mmpt) REVERT: H 46 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8888 (mmmt) REVERT: H 68 ASP cc_start: 0.9528 (t0) cc_final: 0.9223 (t0) REVERT: H 71 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9062 (mm-30) REVERT: H 105 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8195 (tm-30) outliers start: 12 outliers final: 10 residues processed: 221 average time/residue: 0.6919 time to fit residues: 164.1103 Evaluate side-chains 224 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 86 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain H residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 70 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN C 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.056481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.036040 restraints weight = 44986.882| |-----------------------------------------------------------------------------| r_work (start): 0.2594 rms_B_bonded: 2.88 r_work: 0.2390 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12942 Z= 0.243 Angle : 0.699 11.429 18728 Z= 0.389 Chirality : 0.043 0.200 2141 Planarity : 0.004 0.054 1371 Dihedral : 31.292 127.023 4055 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.89 % Allowed : 32.81 % Favored : 65.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.91 (0.31), residues: 772 helix: 2.92 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.53 (0.41), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 79 TYR 0.026 0.002 TYR G 50 PHE 0.013 0.002 PHE F 100 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.24 (12942) covalent geometry : angle 0.69928 / 0.39 (18728) hydrogen bonds : bond 0.04423 / 3.01 ( 796) hydrogen bonds : angle 3.13207 / 2.30 ( 2004) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.72 seconds wall clock time: 66 minutes 34.81 seconds (3994.81 seconds total)