Starting phenix.real_space_refine on Fri Aug 7 05:28:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd0_51238/08_2026/9gd0_51238.cif" } resolution = 2.8 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= -0.005 sd= 1.153 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 500 5.49 5 S 22 5.16 5 C 11144 2.51 5 N 3776 2.21 5 O 4765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20207 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 614 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" 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: "H" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 5090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5090 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "J" Number of atoms: 5160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 5160 Classifications: {'DNA': 250} Link IDs: {'rna3p': 249} Chain: "K" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 592 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "L" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" 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: "N" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "O" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Time building chain proxies: 3.74, per 1000 atoms: 0.19 Number of scatterers: 20207 At special positions: 0 Unit cell: (110.7, 124.23, 188.19, 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 22 16.00 P 500 15.00 O 4765 8.00 N 3776 7.00 C 11144 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: 1.44 Conformation dependent library (CDL) restraints added in 450.6 milliseconds 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 17 sheets defined 75.3% alpha, 3.2% beta 247 base pairs and 498 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.901A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.529A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.530A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.479A 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 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.591A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) 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 removed outlier: 3.621A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.556A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.346A 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 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 removed outlier: 3.665A pdb=" N MET K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 132 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: 4.199A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 97 Processing helix chain 'M' and resid 16 through 22 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 90 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'N' and resid 34 through 46 removed outlier: 3.827A pdb=" N GLN N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 81 removed outlier: 3.646A pdb=" N ILE N 58 " --> pdb=" O LYS N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 99 removed outlier: 3.659A pdb=" N THR N 93 " --> pdb=" O ARG N 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 121 removed outlier: 3.527A pdb=" N SER N 109 " --> pdb=" O LYS N 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 63 through 77 removed outlier: 3.686A pdb=" N ASP O 77 " --> pdb=" O GLU O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.639A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 3.523A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN P 64 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL P 65 " --> pdb=" O PHE P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.869A 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 removed outlier: 6.303A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.941A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.762A 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: 6.976A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (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 Processing sheet with id=AB2, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.773A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.010A pdb=" N ARG M 42 " --> pdb=" O ILE N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AB6, first strand: chain 'M' and resid 100 through 102 Processing sheet with id=AB7, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.852A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'O' and resid 118 through 119 701 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 631 hydrogen bonds 1262 hydrogen bond angles 0 basepair planarities 247 basepair parallelities 498 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4650 1.34 - 1.45: 6452 1.45 - 1.57: 9444 1.57 - 1.69: 998 1.69 - 1.80: 40 Bond restraints: 21584 Sorted by residual: bond pdb=" N ARG F 92 " pdb=" CA ARG F 92 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N GLU H 32 " pdb=" CA GLU H 32 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.15e+00 bond pdb=" N ARG N 83 " pdb=" CA ARG N 83 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.33e-02 5.65e+03 5.98e+00 bond pdb=" N GLU N 32 " pdb=" CA GLU N 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 21579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 30579 1.77 - 3.53: 701 3.53 - 5.30: 23 5.30 - 7.06: 5 7.06 - 8.83: 1 Bond angle restraints: 31309 Sorted by residual: angle pdb=" O3' DA J 90 " pdb=" C3' DA J 90 " pdb=" C2' DA J 90 " ideal model delta sigma weight residual 109.40 100.57 8.83 2.50e+00 1.60e-01 1.25e+01 angle pdb=" C4' DG J 21 " pdb=" O4' DG J 21 " pdb=" C1' DG J 21 " ideal model delta sigma weight residual 110.10 106.59 3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" C4' DG I 20 " pdb=" O4' DG I 20 " pdb=" C1' DG I 20 " ideal model delta sigma weight residual 110.10 106.86 3.24 1.00e+00 1.00e+00 1.05e+01 angle pdb=" C4' DC J 77 " pdb=" O4' DC J 77 " pdb=" C1' DC J 77 " ideal model delta sigma weight residual 110.10 107.03 3.07 1.00e+00 1.00e+00 9.43e+00 angle pdb=" C4' DG I -41 " pdb=" O4' DG I -41 " pdb=" C1' DG I -41 " ideal model delta sigma weight residual 110.10 107.14 2.96 1.00e+00 1.00e+00 8.74e+00 ... (remaining 31304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7573 17.97 - 35.94: 1669 35.94 - 53.91: 2206 53.91 - 71.88: 229 71.88 - 89.85: 10 Dihedral angle restraints: 11687 sinusoidal: 8043 harmonic: 3644 Sorted by residual: dihedral pdb=" CA PRO N 100 " pdb=" C PRO N 100 " pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta harmonic sigma weight residual -180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA PHE O 84 " pdb=" C PHE O 84 " pdb=" N GLN O 85 " pdb=" CA GLN O 85 " ideal model delta harmonic sigma weight residual 180.00 155.61 24.39 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N THR L 30 " pdb=" CA THR L 30 " ideal model delta harmonic sigma weight residual 180.00 -156.59 -23.41 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 11684 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2079 0.038 - 0.076: 1045 0.076 - 0.113: 388 0.113 - 0.151: 63 0.151 - 0.189: 3 Chirality restraints: 3578 Sorted by residual: chirality pdb=" C3' DA J 90 " pdb=" C4' DA J 90 " pdb=" O3' DA J 90 " pdb=" C2' DA J 90 " both_signs ideal model delta sigma weight residual False -2.73 -2.92 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA ILE G 79 " pdb=" N ILE G 79 " pdb=" C ILE G 79 " pdb=" CB ILE G 79 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" C4' DA J 91 " pdb=" C5' DA J 91 " pdb=" O4' DA J 91 " pdb=" C3' DA J 91 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 3575 not shown) Planarity restraints: 2225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 70 " -0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C VAL B 70 " 0.063 2.00e-02 2.50e+03 pdb=" O VAL B 70 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 71 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 67 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C ARG L 67 " 0.061 2.00e-02 2.50e+03 pdb=" O ARG L 67 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP L 68 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 51 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C TYR L 51 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR L 51 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU L 52 " 0.021 2.00e-02 2.50e+03 ... (remaining 2222 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2872 2.76 - 3.30: 16508 3.30 - 3.83: 38423 3.83 - 4.37: 49836 4.37 - 4.90: 69965 Nonbonded interactions: 177604 Sorted by model distance: nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.229 3.040 nonbonded pdb=" OE2 GLU A 50 " pdb=" NH1 ARG B 39 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.346 3.040 nonbonded pdb=" NH1 ARG K 116 " pdb=" O THR K 118 " model vdw 2.358 3.120 nonbonded pdb=" NH1 ARG O 128 " pdb=" OE2 GLU O 133 " model vdw 2.389 3.120 ... (remaining 177599 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' selection = chain 'E' selection = (chain 'O' and resid 39 through 133) } ncs_group { reference = (chain 'B' and resid 25 through 97) selection = (chain 'F' and resid 25 through 97) selection = (chain 'L' and resid 25 through 97) selection = (chain 'P' and resid 25 through 97) } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 120) selection = (chain 'N' and resid 32 through 120) } 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: 2.380 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: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.660 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.005 0.033 21584 Z= 0.286 Angle : 0.693 8.828 31309 Z= 0.507 Chirality : 0.048 0.189 3578 Planarity : 0.012 0.096 2225 Dihedral : 27.261 89.849 9331 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -0.62 (0.21), residues: 1225 helix: -0.35 (0.15), residues: 928 sheet: None (None), residues: 0 loop : -0.03 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG A 63 TYR 0.027 0.005 TYR M 57 PHE 0.016 0.003 PHE D 67 HIS 0.013 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.29 (21584) covalent geometry : angle 0.69265 / 0.51 (31309) hydrogen bonds : bond 0.12128 / 7.97 ( 1332) hydrogen bonds : angle 5.56001 / 3.98 ( 3329) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7508 (tt0) cc_final: 0.7246 (tt0) REVERT: C 57 TYR cc_start: 0.8459 (t80) cc_final: 0.7486 (t80) REVERT: M 114 VAL cc_start: 0.8668 (t) cc_final: 0.8430 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.8951 time to fit residues: 292.9655 Evaluate side-chains 217 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 25 ASN B 75 HIS B 93 GLN D 106 HIS E 93 GLN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 108 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.114077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084430 restraints weight = 45511.110| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.54 r_work: 0.3216 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21584 Z= 0.205 Angle : 0.795 8.436 31309 Z= 0.442 Chirality : 0.051 0.229 3578 Planarity : 0.005 0.058 2225 Dihedral : 30.833 73.833 6859 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.24 % Allowed : 13.44 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.39 (0.23), residues: 1225 helix: 1.30 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.11 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 89 TYR 0.023 0.002 TYR C 57 PHE 0.013 0.002 PHE K 67 HIS 0.007 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (21584) covalent geometry : angle 0.79511 / 0.44 (31309) hydrogen bonds : bond 0.05422 / 3.58 ( 1332) hydrogen bonds : angle 3.23005 / 2.33 ( 3329) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.530 Fit side-chains revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7916 (mp0) REVERT: C 64 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: D 54 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8313 (mtmm) REVERT: D 110 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: D 113 LYS cc_start: 0.9048 (tttt) cc_final: 0.8805 (tttm) REVERT: G 92 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: H 43 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8282 (mmpt) REVERT: H 73 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: H 84 SER cc_start: 0.9189 (m) cc_final: 0.8898 (p) REVERT: K 79 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8328 (tmtt) REVERT: K 120 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: M 61 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (tp30) REVERT: M 73 ASN cc_start: 0.8586 (t0) cc_final: 0.8266 (t0) REVERT: N 102 GLU cc_start: 0.7912 (tp30) cc_final: 0.7687 (tp30) outliers start: 34 outliers final: 14 residues processed: 235 average time/residue: 0.9099 time to fit residues: 232.9710 Evaluate side-chains 239 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain O residue 64 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 158 optimal weight: 0.6980 chunk 96 optimal weight: 40.0000 chunk 108 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 26 optimal weight: 0.2980 chunk 75 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 105 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 64 ASN B 93 GLN D 46 HIS D 106 HIS L 25 ASN M 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.110173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.080185 restraints weight = 45695.156| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.56 r_work: 0.3129 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 21584 Z= 0.410 Angle : 0.873 8.772 31309 Z= 0.472 Chirality : 0.059 0.277 3578 Planarity : 0.007 0.066 2225 Dihedral : 31.587 72.946 6859 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.96 % Allowed : 13.92 % Favored : 81.12 % 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: 0.80 (0.22), residues: 1225 helix: 0.97 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 39 TYR 0.020 0.003 TYR E 54 PHE 0.018 0.003 PHE K 67 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00881 / 0.41 (21584) covalent geometry : angle 0.87253 / 0.47 (31309) hydrogen bonds : bond 0.08448 / 5.64 ( 1332) hydrogen bonds : angle 3.42233 / 2.47 ( 3329) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 225 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8991 (ttm-80) cc_final: 0.8691 (ttm-80) REVERT: C 57 TYR cc_start: 0.9143 (t80) cc_final: 0.8399 (t80) REVERT: C 61 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: C 64 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8427 (tp30) REVERT: C 102 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 54 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8510 (mtmm) REVERT: D 110 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: D 113 LYS cc_start: 0.9103 (tttt) cc_final: 0.8854 (tttm) REVERT: F 92 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8556 (ttm-80) REVERT: G 73 ASN cc_start: 0.8686 (m-40) cc_final: 0.8212 (m-40) REVERT: G 92 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: G 104 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: H 44 GLN cc_start: 0.9081 (tt0) cc_final: 0.8840 (mt0) REVERT: H 73 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: K 79 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7731 (tmtt) REVERT: M 73 ASN cc_start: 0.8705 (t0) cc_final: 0.8227 (t0) REVERT: P 95 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8173 (ptp90) outliers start: 52 outliers final: 21 residues processed: 240 average time/residue: 0.8637 time to fit residues: 225.2265 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 95 optimal weight: 50.0000 chunk 29 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 161 optimal weight: 0.6980 chunk 33 optimal weight: 0.1980 chunk 96 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 46 HIS D 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.112726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.082738 restraints weight = 45571.001| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.55 r_work: 0.3193 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21584 Z= 0.147 Angle : 0.711 8.204 31309 Z= 0.401 Chirality : 0.048 0.250 3578 Planarity : 0.005 0.051 2225 Dihedral : 31.433 73.810 6859 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 4.00 % Allowed : 15.25 % Favored : 80.74 % 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: 1.69 (0.23), residues: 1225 helix: 1.63 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.48 (0.32), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 99 TYR 0.019 0.002 TYR L 51 PHE 0.011 0.001 PHE B 61 HIS 0.007 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.15 (21584) covalent geometry : angle 0.71083 / 0.40 (31309) hydrogen bonds : bond 0.04709 / 3.10 ( 1332) hydrogen bonds : angle 3.06157 / 2.20 ( 3329) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9124 (t80) cc_final: 0.8247 (t80) REVERT: C 61 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: C 64 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8321 (tp30) REVERT: D 54 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8444 (mtmm) REVERT: D 110 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: F 92 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8299 (ttm-80) REVERT: F 93 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: G 73 ASN cc_start: 0.8579 (m-40) cc_final: 0.8152 (m-40) REVERT: G 104 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: K 79 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7657 (tmtt) REVERT: K 120 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8160 (mtt) REVERT: M 61 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8473 (tp30) REVERT: M 73 ASN cc_start: 0.8605 (t0) cc_final: 0.8246 (t0) REVERT: P 95 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8251 (ptp90) outliers start: 42 outliers final: 14 residues processed: 248 average time/residue: 0.8724 time to fit residues: 235.4017 Evaluate side-chains 243 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 120 MET Chi-restraints excluded: chain M residue 61 GLU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 16 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 95 optimal weight: 50.0000 chunk 57 optimal weight: 0.9980 chunk 168 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN D 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.112591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082887 restraints weight = 45490.465| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.54 r_work: 0.3188 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21584 Z= 0.163 Angle : 0.668 9.996 31309 Z= 0.382 Chirality : 0.045 0.238 3578 Planarity : 0.005 0.039 2225 Dihedral : 31.105 73.084 6859 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.91 % Allowed : 16.40 % Favored : 79.69 % 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: 2.01 (0.23), residues: 1225 helix: 1.86 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.39 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.018 0.002 TYR N 80 PHE 0.014 0.001 PHE O 78 HIS 0.006 0.001 HIS N 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (21584) covalent geometry : angle 0.66802 / 0.38 (31309) hydrogen bonds : bond 0.04516 / 3.00 ( 1332) hydrogen bonds : angle 2.95023 / 2.12 ( 3329) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 231 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8716 (m110) REVERT: B 35 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8597 (mtp85) REVERT: C 57 TYR cc_start: 0.9134 (t80) cc_final: 0.8154 (t80) REVERT: C 61 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 64 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8291 (tp30) REVERT: C 102 ILE cc_start: 0.9517 (OUTLIER) cc_final: 0.9018 (mp) REVERT: D 54 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8446 (mtmm) REVERT: D 110 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8134 (tp30) REVERT: F 92 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8397 (ttm-80) REVERT: F 93 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: G 92 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: H 43 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8505 (ttmm) REVERT: H 73 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8190 (tm-30) REVERT: K 79 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7696 (tmtt) REVERT: M 90 ASP cc_start: 0.8288 (t0) cc_final: 0.8011 (t0) REVERT: N 39 TYR cc_start: 0.8112 (t80) cc_final: 0.7897 (t80) REVERT: N 102 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8125 (tp30) REVERT: O 94 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: P 95 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8326 (ptp90) outliers start: 41 outliers final: 14 residues processed: 243 average time/residue: 0.7989 time to fit residues: 211.1198 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 78 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 165 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 93 GLN D 106 HIS G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083893 restraints weight = 45524.133| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.53 r_work: 0.3213 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21584 Z= 0.142 Angle : 0.650 10.467 31309 Z= 0.375 Chirality : 0.044 0.234 3578 Planarity : 0.004 0.037 2225 Dihedral : 30.980 72.621 6859 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.53 % Allowed : 17.35 % Favored : 79.12 % 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: 2.26 (0.23), residues: 1225 helix: 2.06 (0.17), residues: 937 sheet: None (None), residues: 0 loop : -0.34 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 35 TYR 0.026 0.002 TYR B 88 PHE 0.014 0.001 PHE O 78 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (21584) covalent geometry : angle 0.64999 / 0.37 (31309) hydrogen bonds : bond 0.03985 / 2.65 ( 1332) hydrogen bonds : angle 2.87276 / 2.07 ( 3329) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8838 (mtp85) cc_final: 0.8632 (mtp85) REVERT: B 67 ARG cc_start: 0.8927 (ttm-80) cc_final: 0.8705 (ttm110) REVERT: C 57 TYR cc_start: 0.9133 (t80) cc_final: 0.8080 (t80) REVERT: C 61 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: C 64 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: C 102 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9013 (mp) REVERT: D 110 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: F 92 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8366 (ttm-80) REVERT: F 93 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: H 43 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8484 (ttmm) REVERT: H 73 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8128 (tm-30) REVERT: K 79 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7672 (tmtt) REVERT: K 133 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5265 (mp0) REVERT: N 39 TYR cc_start: 0.8176 (t80) cc_final: 0.7892 (t80) REVERT: N 43 LYS cc_start: 0.9039 (tppt) cc_final: 0.8838 (mmtm) REVERT: N 56 MET cc_start: 0.9054 (tpp) cc_final: 0.8837 (tpp) REVERT: N 102 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8106 (tp30) REVERT: P 95 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8402 (ptp90) outliers start: 37 outliers final: 12 residues processed: 245 average time/residue: 0.8474 time to fit residues: 226.2664 Evaluate side-chains 243 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Chi-restraints excluded: chain P residue 95 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 80 optimal weight: 20.0000 chunk 159 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 74 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 157 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 106 HIS G 104 GLN L 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.113250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083865 restraints weight = 45679.919| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.54 r_work: 0.3211 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21584 Z= 0.149 Angle : 0.649 10.894 31309 Z= 0.375 Chirality : 0.043 0.233 3578 Planarity : 0.004 0.071 2225 Dihedral : 30.858 72.063 6859 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.05 % Allowed : 18.78 % Favored : 78.17 % 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: 2.35 (0.23), residues: 1225 helix: 2.13 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 78 TYR 0.018 0.002 TYR B 88 PHE 0.010 0.001 PHE K 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (21584) covalent geometry : angle 0.64864 / 0.37 (31309) hydrogen bonds : bond 0.03969 / 2.64 ( 1332) hydrogen bonds : angle 2.85257 / 2.05 ( 3329) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8615 (mtp85) REVERT: C 57 TYR cc_start: 0.9147 (t80) cc_final: 0.8077 (t80) REVERT: C 61 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: C 64 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8255 (tp30) REVERT: C 102 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9114 (mp) REVERT: D 110 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8126 (tp30) REVERT: F 92 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.8395 (ttm-80) REVERT: F 93 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: H 43 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8475 (ttmm) REVERT: H 73 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: K 79 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7666 (tmtt) REVERT: M 73 ASN cc_start: 0.8469 (t0) cc_final: 0.8171 (t0) REVERT: M 90 ASP cc_start: 0.8212 (t0) cc_final: 0.7958 (t0) REVERT: N 39 TYR cc_start: 0.8125 (t80) cc_final: 0.7922 (t80) REVERT: N 43 LYS cc_start: 0.9075 (tppt) cc_final: 0.8873 (mmtm) REVERT: N 73 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8378 (mm-30) REVERT: N 102 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8167 (tp30) REVERT: P 95 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8427 (ptp90) outliers start: 32 outliers final: 14 residues processed: 241 average time/residue: 0.8097 time to fit residues: 212.2915 Evaluate side-chains 246 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 222 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 101 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 106 HIS G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.113430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083959 restraints weight = 45547.092| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.56 r_work: 0.3216 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21584 Z= 0.149 Angle : 0.641 11.299 31309 Z= 0.371 Chirality : 0.043 0.230 3578 Planarity : 0.004 0.051 2225 Dihedral : 30.748 71.922 6859 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.24 % Allowed : 19.07 % Favored : 77.69 % 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: 2.46 (0.23), residues: 1225 helix: 2.21 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.30 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 78 TYR 0.023 0.002 TYR B 88 PHE 0.011 0.001 PHE K 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.15 (21584) covalent geometry : angle 0.64067 / 0.37 (31309) hydrogen bonds : bond 0.03920 / 2.60 ( 1332) hydrogen bonds : angle 2.82728 / 2.03 ( 3329) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 231 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8619 (mtp85) REVERT: C 57 TYR cc_start: 0.9149 (t80) cc_final: 0.8083 (t80) REVERT: C 61 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 64 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8249 (tp30) REVERT: C 102 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9131 (mp) REVERT: D 73 GLU cc_start: 0.9056 (tp30) cc_final: 0.8828 (mm-30) REVERT: F 92 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8395 (ttm-80) REVERT: F 93 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: H 43 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8461 (ttmm) REVERT: H 73 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: K 79 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7664 (tmtt) REVERT: K 133 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5488 (mp0) REVERT: N 39 TYR cc_start: 0.8196 (t80) cc_final: 0.7983 (t80) REVERT: N 73 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8423 (mm-30) REVERT: N 102 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8145 (tp30) REVERT: P 95 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8456 (ptp90) outliers start: 34 outliers final: 13 residues processed: 241 average time/residue: 0.8876 time to fit residues: 232.8890 Evaluate side-chains 242 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 95 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 93 optimal weight: 50.0000 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN D 106 HIS G 104 GLN L 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.083932 restraints weight = 45496.859| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.55 r_work: 0.3220 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21584 Z= 0.149 Angle : 0.649 13.167 31309 Z= 0.375 Chirality : 0.042 0.227 3578 Planarity : 0.004 0.047 2225 Dihedral : 30.661 72.010 6859 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 2.48 % Allowed : 20.11 % Favored : 77.41 % 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: 2.52 (0.23), residues: 1225 helix: 2.24 (0.16), residues: 937 sheet: None (None), residues: 0 loop : -0.21 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG P 78 TYR 0.020 0.002 TYR B 88 PHE 0.010 0.001 PHE K 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (21584) covalent geometry : angle 0.64872 / 0.38 (31309) hydrogen bonds : bond 0.03846 / 2.56 ( 1332) hydrogen bonds : angle 2.80849 / 2.01 ( 3329) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8105 (pt0) cc_final: 0.7893 (pt0) REVERT: C 61 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: C 64 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8232 (tp30) REVERT: C 102 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9149 (mp) REVERT: F 91 LYS cc_start: 0.9137 (ttpt) cc_final: 0.8850 (tttt) REVERT: F 92 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8237 (ttm-80) REVERT: F 93 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7390 (mp10) REVERT: H 43 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8464 (ttmm) REVERT: K 79 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7683 (tmtt) REVERT: K 133 GLU cc_start: 0.6174 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: N 73 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8387 (mm-30) REVERT: N 102 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8113 (tp30) REVERT: P 95 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8490 (ptp90) outliers start: 26 outliers final: 13 residues processed: 234 average time/residue: 0.8375 time to fit residues: 213.7172 Evaluate side-chains 240 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 0.0970 chunk 18 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 142 optimal weight: 0.0070 chunk 146 optimal weight: 0.6980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS G 104 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.113903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084575 restraints weight = 45866.447| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.56 r_work: 0.3228 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21584 Z= 0.141 Angle : 0.650 10.787 31309 Z= 0.376 Chirality : 0.042 0.227 3578 Planarity : 0.004 0.064 2225 Dihedral : 30.644 72.016 6859 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.57 % Allowed : 20.21 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.23), residues: 1225 helix: 2.28 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 35 TYR 0.044 0.002 TYR B 88 PHE 0.010 0.001 PHE K 67 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (21584) covalent geometry : angle 0.64954 / 0.38 (31309) hydrogen bonds : bond 0.03723 / 2.48 ( 1332) hydrogen bonds : angle 2.79971 / 2.01 ( 3329) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2450 Ramachandran restraints generated. 1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9088 (t80) cc_final: 0.8040 (t80) REVERT: C 61 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: D 110 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: F 92 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8209 (ttm-80) REVERT: F 93 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: G 104 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8348 (mt0) REVERT: H 43 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (ttmm) REVERT: K 79 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7641 (tmtt) REVERT: K 133 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: N 73 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8414 (mm-30) REVERT: N 102 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8107 (tp30) REVERT: O 94 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: P 95 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8491 (ptp90) outliers start: 27 outliers final: 12 residues processed: 232 average time/residue: 0.8524 time to fit residues: 215.5711 Evaluate side-chains 240 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 44 GLN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 133 GLU Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 95 ARG Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 106 HIS ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.113905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.084868 restraints weight = 45410.427| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.53 r_work: 0.3234 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.218 21584 Z= 0.250 Angle : 0.881 59.154 31309 Z= 0.513 Chirality : 0.043 0.324 3578 Planarity : 0.006 0.209 2225 Dihedral : 30.642 72.012 6859 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.10 % Allowed : 20.97 % Favored : 76.93 % Cbeta Deviations : 0.17 % 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: 2.57 (0.23), residues: 1225 helix: 2.27 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 35 TYR 0.035 0.002 TYR B 88 PHE 0.010 0.001 PHE K 67 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.25 (21584) covalent geometry : angle 0.88074 / 0.51 (31309) hydrogen bonds : bond 0.03752 / 2.50 ( 1332) hydrogen bonds : angle 2.80996 / 2.02 ( 3329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8327.35 seconds wall clock time: 141 minutes 39.10 seconds (8499.10 seconds total)