Starting phenix.real_space_refine on Thu Sep 18 19:58:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd0_51238/09_2025/9gd0_51238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd0_51238/09_2025/9gd0_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_51238/09_2025/9gd0_51238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd0_51238/09_2025/9gd0_51238.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd0_51238/09_2025/9gd0_51238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd0_51238/09_2025/9gd0_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-2.0-5805/lib/python3.9/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: 4.49, per 1000 atoms: 0.22 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: 1.92 Conformation dependent library (CDL) restraints added in 571.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.37 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: 4.40 Time building geometry restraints manager: 2.53 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 - 2.19: 30386 2.19 - 4.37: 901 4.37 - 6.56: 16 6.56 - 8.74: 2 8.74 - 10.93: 4 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 111.50 100.57 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" O3' DC J 76 " pdb=" C3' DC J 76 " pdb=" C2' DC J 76 " ideal model delta sigma weight residual 111.50 102.60 8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" O3' DA I -57 " pdb=" C3' DA I -57 " pdb=" C2' DA I -57 " ideal model delta sigma weight residual 111.50 102.66 8.84 1.50e+00 4.44e-01 3.47e+01 angle pdb=" O3' DG I -56 " pdb=" C3' DG I -56 " pdb=" C2' DG I -56 " ideal model delta sigma weight residual 111.50 102.69 8.81 1.50e+00 4.44e-01 3.45e+01 angle pdb=" O3' DC J 75 " pdb=" C3' DC J 75 " pdb=" C2' DC J 75 " ideal model delta sigma weight residual 111.50 102.81 8.69 1.50e+00 4.44e-01 3.36e+01 ... (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 - 0.052: 2426 0.052 - 0.104: 949 0.104 - 0.156: 188 0.156 - 0.208: 12 0.208 - 0.259: 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 -2.66 -2.92 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' DC J 76 " pdb=" C4' DC J 76 " pdb=" O3' DC J 76 " pdb=" C2' DC J 76 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C3' DC J 75 " pdb=" C4' DC J 75 " pdb=" O3' DC J 75 " pdb=" C2' DC J 75 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.16e+00 ... (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: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.340 Find NCS groups from input model: 0.200 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:10.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 0.033 21584 Z= 0.261 Angle : 0.842 10.928 31309 Z= 0.545 Chirality : 0.054 0.259 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 aren 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 covalent geometry : bond 0.00581 (21584) covalent geometry : angle 0.84181 (31309) hydrogen bonds : bond 0.12128 ( 1332) hydrogen bonds : angle 5.56001 ( 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 : 0.414 Fit side-chains revert: symmetry clash 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: 0.8428 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.8858 time to fit residues: 287.6812 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 : 0.477 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 5.9990 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 25 ASN B 93 GLN D 106 HIS E 93 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.113394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.083740 restraints weight = 45595.305| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.55 r_work: 0.3208 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21584 Z= 0.235 Angle : 0.634 6.842 31309 Z= 0.384 Chirality : 0.036 0.150 3578 Planarity : 0.005 0.051 2225 Dihedral : 30.792 71.136 6859 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.34 % Allowed : 12.77 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.23), residues: 1225 helix: 1.50 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.20 (0.32), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.015 0.002 TYR B 51 PHE 0.010 0.002 PHE K 78 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00529 (21584) covalent geometry : angle 0.63426 (31309) hydrogen bonds : bond 0.04655 ( 1332) hydrogen bonds : angle 2.99274 ( 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 277 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8919 (tp40) cc_final: 0.8641 (tp-100) REVERT: B 67 ARG cc_start: 0.8937 (ttm-80) cc_final: 0.8638 (ttm110) REVERT: C 57 TYR cc_start: 0.9124 (t80) cc_final: 0.8157 (t80) REVERT: C 61 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: C 64 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: C 73 ASN cc_start: 0.8257 (t0) cc_final: 0.8032 (t0) REVERT: C 95 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.9116 (ttpp) REVERT: D 54 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8384 (mtmm) REVERT: D 110 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: D 113 LYS cc_start: 0.9074 (tttt) cc_final: 0.8829 (tttm) REVERT: G 41 GLU cc_start: 0.8353 (pm20) cc_final: 0.7654 (pm20) REVERT: H 43 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: H 44 GLN cc_start: 0.9000 (tt0) cc_final: 0.8789 (mt0) REVERT: H 113 LYS cc_start: 0.8727 (ttmt) cc_final: 0.8520 (ttpt) REVERT: K 79 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7617 (tmtt) REVERT: L 79 LYS cc_start: 0.8985 (mttm) cc_final: 0.8776 (mmmt) REVERT: M 61 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8424 (tp30) REVERT: M 73 ASN cc_start: 0.8677 (t0) cc_final: 0.8282 (t0) REVERT: M 95 LYS cc_start: 0.9100 (ttmp) cc_final: 0.8811 (tppp) REVERT: O 90 MET cc_start: 0.8444 (mtp) cc_final: 0.7839 (mtp) REVERT: P 95 ARG cc_start: 0.8092 (mtt-85) cc_final: 0.7879 (ptp90) outliers start: 35 outliers final: 10 residues processed: 250 average time/residue: 0.9005 time to fit residues: 243.7658 Evaluate side-chains 239 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 221 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 95 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 101 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain M residue 61 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 158 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 chunk 105 optimal weight: 3.9990 chunk 93 optimal weight: 30.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN D 46 HIS D 106 HIS ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.111882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082670 restraints weight = 45769.497| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.52 r_work: 0.3182 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 21584 Z= 0.251 Angle : 0.606 7.648 31309 Z= 0.365 Chirality : 0.036 0.162 3578 Planarity : 0.005 0.042 2225 Dihedral : 30.359 72.240 6859 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.62 % Allowed : 14.87 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.23), residues: 1225 helix: 1.79 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.31 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.013 0.002 TYR B 88 PHE 0.014 0.002 PHE O 78 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00571 (21584) covalent geometry : angle 0.60589 (31309) hydrogen bonds : bond 0.04611 ( 1332) hydrogen bonds : angle 2.91301 ( 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 271 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.7422 (pm20) cc_final: 0.6709 (pm20) REVERT: C 57 TYR cc_start: 0.9166 (t80) cc_final: 0.8204 (t80) REVERT: C 61 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: C 64 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8342 (tp30) REVERT: C 102 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.8995 (mp) REVERT: D 118 TYR cc_start: 0.9268 (t80) cc_final: 0.9016 (t80) REVERT: E 59 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: F 92 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8335 (ttm-80) REVERT: F 93 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: H 113 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8545 (ttpt) REVERT: K 90 MET cc_start: 0.8747 (mmm) cc_final: 0.8541 (mmm) REVERT: M 73 ASN cc_start: 0.8641 (t0) cc_final: 0.8196 (t0) REVERT: O 41 TYR cc_start: 0.8870 (m-80) cc_final: 0.8576 (m-80) REVERT: O 90 MET cc_start: 0.8332 (mtp) cc_final: 0.7422 (mtp) REVERT: O 94 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: P 95 ARG cc_start: 0.8130 (mtt-85) cc_final: 0.7885 (ptp90) outliers start: 38 outliers final: 16 residues processed: 244 average time/residue: 0.9096 time to fit residues: 240.4225 Evaluate side-chains 238 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 93 GLN 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 E residue 58 THR Chi-restraints excluded: chain E residue 59 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 54 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 48 ASP Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 80 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 95 optimal weight: 10.0000 chunk 29 optimal weight: 0.6980 chunk 140 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.113091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.083588 restraints weight = 45819.439| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.55 r_work: 0.3212 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21584 Z= 0.177 Angle : 0.571 8.426 31309 Z= 0.348 Chirality : 0.033 0.148 3578 Planarity : 0.004 0.040 2225 Dihedral : 30.202 71.950 6859 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.24 % Allowed : 15.92 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.23), residues: 1225 helix: 2.14 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.31 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.013 0.002 TYR N 80 PHE 0.017 0.001 PHE O 78 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00393 (21584) covalent geometry : angle 0.57103 (31309) hydrogen bonds : bond 0.03626 ( 1332) hydrogen bonds : angle 2.73027 ( 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 275 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9171 (t80) cc_final: 0.8122 (t80) REVERT: C 61 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: C 64 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8259 (tp30) REVERT: C 102 ILE cc_start: 0.9493 (OUTLIER) cc_final: 0.8992 (mp) REVERT: D 110 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: D 118 TYR cc_start: 0.9259 (t80) cc_final: 0.8986 (t80) REVERT: F 92 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8147 (ttm-80) REVERT: F 93 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: G 41 GLU cc_start: 0.8150 (pm20) cc_final: 0.7589 (pm20) REVERT: K 79 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.7684 (tmtt) REVERT: M 73 ASN cc_start: 0.8630 (t0) cc_final: 0.8252 (t0) REVERT: O 90 MET cc_start: 0.8296 (mtp) cc_final: 0.7302 (mtp) REVERT: O 94 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7596 (mp0) outliers start: 34 outliers final: 11 residues processed: 248 average time/residue: 0.8744 time to fit residues: 234.9040 Evaluate side-chains 241 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 E residue 58 THR 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 54 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain P residue 46 ILE 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: 4.9990 chunk 98 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.112991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.083300 restraints weight = 45474.840| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.55 r_work: 0.3203 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21584 Z= 0.195 Angle : 0.575 10.220 31309 Z= 0.349 Chirality : 0.034 0.154 3578 Planarity : 0.004 0.038 2225 Dihedral : 30.064 70.800 6859 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.34 % Allowed : 17.92 % Favored : 78.74 % 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 aren not related in a simple way. whole: 2.52 (0.23), residues: 1225 helix: 2.24 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -0.25 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 35 TYR 0.017 0.002 TYR B 88 PHE 0.011 0.001 PHE K 67 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00438 (21584) covalent geometry : angle 0.57458 (31309) hydrogen bonds : bond 0.03875 ( 1332) hydrogen bonds : angle 2.72240 ( 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 273 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8853 (tp40) cc_final: 0.8522 (tp-100) REVERT: B 25 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8699 (m110) REVERT: C 57 TYR cc_start: 0.9179 (t80) cc_final: 0.8150 (t80) REVERT: C 61 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: C 64 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: C 75 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8549 (mmtt) REVERT: C 102 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9001 (mp) REVERT: D 110 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: F 92 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8202 (ttm-80) REVERT: H 43 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8568 (tppt) REVERT: K 73 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6977 (mm-30) REVERT: K 79 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7694 (tmtt) REVERT: M 73 ASN cc_start: 0.8647 (t0) cc_final: 0.8271 (t0) REVERT: M 95 LYS cc_start: 0.9126 (ttmp) cc_final: 0.8840 (tppp) REVERT: O 90 MET cc_start: 0.8277 (mtp) cc_final: 0.7415 (mtp) REVERT: O 94 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7673 (mp0) outliers start: 35 outliers final: 13 residues processed: 248 average time/residue: 0.8592 time to fit residues: 231.3992 Evaluate side-chains 243 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 222 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 84 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain O residue 94 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 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 37 optimal weight: 0.9980 chunk 151 optimal weight: 0.7980 chunk 55 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 48 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN N 81 ASN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.113722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.084587 restraints weight = 45401.347| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.53 r_work: 0.3228 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21584 Z= 0.161 Angle : 0.573 10.219 31309 Z= 0.346 Chirality : 0.033 0.149 3578 Planarity : 0.004 0.054 2225 Dihedral : 30.024 70.794 6859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.86 % Allowed : 18.11 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.23), residues: 1225 helix: 2.39 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.18 (0.34), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.023 0.002 TYR B 88 PHE 0.009 0.001 PHE A 67 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00352 (21584) covalent geometry : angle 0.57318 (31309) hydrogen bonds : bond 0.03448 ( 1332) hydrogen bonds : angle 2.67185 ( 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 261 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9158 (t80) cc_final: 0.8104 (t80) REVERT: C 61 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: C 64 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: D 110 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: F 92 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8175 (ttm-80) REVERT: G 41 GLU cc_start: 0.8155 (pm20) cc_final: 0.7515 (pm20) REVERT: K 79 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7675 (tmtt) REVERT: K 133 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.4972 (mp0) REVERT: O 90 MET cc_start: 0.8230 (mtp) cc_final: 0.7456 (mtp) REVERT: O 94 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7609 (mp0) outliers start: 30 outliers final: 13 residues processed: 242 average time/residue: 0.8391 time to fit residues: 220.4748 Evaluate side-chains 241 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 54 LYS 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 N residue 43 LYS 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 46 ILE Chi-restraints excluded: chain P residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 80 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 157 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.112466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.083031 restraints weight = 45582.440| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.54 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 21584 Z= 0.210 Angle : 0.593 11.418 31309 Z= 0.356 Chirality : 0.035 0.153 3578 Planarity : 0.004 0.042 2225 Dihedral : 30.087 70.705 6859 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.76 % Allowed : 19.16 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.61 (0.23), residues: 1225 helix: 2.29 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.18 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 78 TYR 0.025 0.002 TYR B 88 PHE 0.013 0.001 PHE K 67 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00473 (21584) covalent geometry : angle 0.59340 (31309) hydrogen bonds : bond 0.04112 ( 1332) hydrogen bonds : angle 2.76927 ( 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 264 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 235 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8821 (m-40) cc_final: 0.8487 (m110) REVERT: B 35 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8667 (mtp85) REVERT: C 57 TYR cc_start: 0.9151 (t80) cc_final: 0.8141 (t80) REVERT: C 61 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: C 64 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8234 (tp30) REVERT: C 102 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.8991 (mp) REVERT: E 59 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7271 (pp20) REVERT: F 92 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8363 (ttm-80) REVERT: F 93 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7624 (mp10) REVERT: G 41 GLU cc_start: 0.8246 (pm20) cc_final: 0.7871 (pm20) REVERT: H 73 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8501 (mm-30) REVERT: K 79 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7674 (tmtt) REVERT: L 84 MET cc_start: 0.8670 (mmm) cc_final: 0.8465 (tpp) REVERT: M 73 ASN cc_start: 0.8740 (t0) cc_final: 0.8464 (t0) REVERT: M 90 ASP cc_start: 0.8315 (t0) cc_final: 0.8041 (t0) REVERT: O 90 MET cc_start: 0.8256 (mtp) cc_final: 0.7448 (mtp) REVERT: O 94 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7694 (mp0) outliers start: 29 outliers final: 13 residues processed: 244 average time/residue: 0.8780 time to fit residues: 232.2872 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 E residue 59 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 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 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 46 ILE 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: 2.9990 chunk 148 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN D 46 HIS D 106 HIS G 104 GLN ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.113003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.083819 restraints weight = 45431.493| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.52 r_work: 0.3216 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21584 Z= 0.174 Angle : 0.600 10.849 31309 Z= 0.359 Chirality : 0.033 0.173 3578 Planarity : 0.005 0.056 2225 Dihedral : 30.086 70.722 6859 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.05 % Allowed : 18.97 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.23), residues: 1225 helix: 2.32 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.16 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 78 TYR 0.033 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 covalent geometry : bond 0.00387 (21584) covalent geometry : angle 0.60049 (31309) hydrogen bonds : bond 0.03848 ( 1332) hydrogen bonds : angle 2.76279 ( 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 263 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8633 (mtp85) REVERT: C 57 TYR cc_start: 0.9135 (t80) cc_final: 0.8129 (t80) REVERT: C 61 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: C 64 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8198 (tp30) REVERT: C 102 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.9066 (mp) REVERT: E 59 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7250 (pp20) REVERT: F 92 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8392 (ttm-80) REVERT: F 93 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7614 (mp10) REVERT: G 41 GLU cc_start: 0.8186 (pm20) cc_final: 0.7854 (pm20) REVERT: H 43 LYS cc_start: 0.8811 (tppt) cc_final: 0.8512 (mmtm) REVERT: H 65 ASP cc_start: 0.9183 (t0) cc_final: 0.8948 (t0) REVERT: H 73 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: K 79 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7669 (tmtt) REVERT: K 133 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: L 52 GLU cc_start: 0.7740 (mp0) cc_final: 0.7468 (mp0) REVERT: M 73 ASN cc_start: 0.8739 (t0) cc_final: 0.8245 (t0) REVERT: O 90 MET cc_start: 0.8230 (mtp) cc_final: 0.7398 (mtp) REVERT: O 94 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7649 (mp0) outliers start: 32 outliers final: 14 residues processed: 240 average time/residue: 0.8605 time to fit residues: 224.0241 Evaluate side-chains 250 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 E residue 58 THR Chi-restraints excluded: chain E residue 59 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 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 N residue 43 LYS 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 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 154 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 2 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS G 104 GLN N 106 HIS O 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.113087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.083675 restraints weight = 45402.466| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.55 r_work: 0.3212 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21584 Z= 0.178 Angle : 0.595 11.206 31309 Z= 0.356 Chirality : 0.034 0.146 3578 Planarity : 0.005 0.067 2225 Dihedral : 30.057 70.694 6859 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.86 % Allowed : 18.78 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.23), residues: 1225 helix: 2.33 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.15 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 78 TYR 0.047 0.002 TYR B 88 PHE 0.009 0.001 PHE A 67 HIS 0.006 0.001 HIS N 106 Details of bonding type rmsd covalent geometry : bond 0.00396 (21584) covalent geometry : angle 0.59511 (31309) hydrogen bonds : bond 0.03674 ( 1332) hydrogen bonds : angle 2.75491 ( 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 258 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8620 (mtp85) REVERT: C 57 TYR cc_start: 0.9139 (t80) cc_final: 0.8118 (t80) REVERT: C 61 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: C 64 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8197 (tp30) REVERT: C 102 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9080 (mp) REVERT: D 110 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: E 59 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: E 133 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7651 (mt-10) REVERT: F 92 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.8400 (ttm-80) REVERT: F 93 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: G 41 GLU cc_start: 0.8185 (pm20) cc_final: 0.7865 (pm20) REVERT: H 43 LYS cc_start: 0.8817 (tppt) cc_final: 0.8404 (mmpt) REVERT: H 65 ASP cc_start: 0.9208 (t0) cc_final: 0.8976 (t0) REVERT: H 73 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: K 79 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7676 (tmtt) REVERT: K 133 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5282 (mp0) REVERT: L 52 GLU cc_start: 0.7744 (mp0) cc_final: 0.7473 (mp0) REVERT: M 73 ASN cc_start: 0.8762 (t0) cc_final: 0.8223 (t0) REVERT: O 90 MET cc_start: 0.8258 (mtp) cc_final: 0.7426 (mtp) REVERT: O 94 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: P 78 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8107 (mtm110) outliers start: 30 outliers final: 16 residues processed: 238 average time/residue: 0.8624 time to fit residues: 222.2399 Evaluate side-chains 252 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 225 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 D residue 110 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 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 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 N residue 43 LYS Chi-restraints excluded: chain O residue 68 GLN Chi-restraints excluded: chain O residue 79 LYS 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 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 65 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS 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 = 0.3964 r_free = 0.3964 target = 0.113355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084032 restraints weight = 45852.162| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.54 r_work: 0.3218 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21584 Z= 0.172 Angle : 0.599 11.424 31309 Z= 0.357 Chirality : 0.033 0.154 3578 Planarity : 0.004 0.057 2225 Dihedral : 30.030 70.623 6859 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.57 % Allowed : 19.35 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.66 (0.23), residues: 1225 helix: 2.32 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.11 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG P 78 TYR 0.054 0.002 TYR B 88 PHE 0.010 0.001 PHE O 78 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00382 (21584) covalent geometry : angle 0.59873 (31309) hydrogen bonds : bond 0.03580 ( 1332) hydrogen bonds : angle 2.74321 ( 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 256 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 ARG cc_start: 0.8886 (mtp85) cc_final: 0.8634 (mtp85) REVERT: C 57 TYR cc_start: 0.9136 (t80) cc_final: 0.8087 (t80) REVERT: C 61 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7771 (mp0) REVERT: C 64 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: C 102 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9072 (mp) REVERT: D 110 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: E 59 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7232 (pp20) REVERT: E 133 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7652 (mt-10) REVERT: F 92 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8383 (ttm-80) REVERT: F 93 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: G 41 GLU cc_start: 0.8169 (pm20) cc_final: 0.7866 (pm20) REVERT: H 43 LYS cc_start: 0.8816 (tppt) cc_final: 0.8413 (mmpt) REVERT: H 65 ASP cc_start: 0.9189 (t0) cc_final: 0.8958 (t0) REVERT: H 73 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8169 (tm-30) REVERT: K 79 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7657 (tmtt) REVERT: K 133 GLU cc_start: 0.6321 (OUTLIER) cc_final: 0.5298 (mp0) REVERT: L 52 GLU cc_start: 0.7778 (mp0) cc_final: 0.7568 (mp0) REVERT: M 73 ASN cc_start: 0.8729 (t0) cc_final: 0.8247 (t0) REVERT: N 56 MET cc_start: 0.9068 (tpp) cc_final: 0.8844 (tpp) REVERT: O 90 MET cc_start: 0.8242 (mtp) cc_final: 0.7431 (mtp) REVERT: O 94 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7651 (mp0) outliers start: 27 outliers final: 14 residues processed: 236 average time/residue: 0.8740 time to fit residues: 223.9872 Evaluate side-chains 248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 D residue 110 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 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 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 79 LYS 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 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: 4.9990 chunk 165 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 168 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS 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 = 0.3957 r_free = 0.3957 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.083213 restraints weight = 45454.671| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.55 r_work: 0.3211 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3546 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= 0.190 Angle : 0.597 11.611 31309 Z= 0.357 Chirality : 0.034 0.172 3578 Planarity : 0.004 0.053 2225 Dihedral : 29.988 70.374 6859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.48 % Allowed : 19.45 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.23), residues: 1225 helix: 2.31 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.11 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 78 TYR 0.038 0.002 TYR B 88 PHE 0.011 0.001 PHE K 67 HIS 0.004 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00426 (21584) covalent geometry : angle 0.59729 (31309) hydrogen bonds : bond 0.03843 ( 1332) hydrogen bonds : angle 2.77218 ( 3329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8466.54 seconds wall clock time: 144 minutes 0.49 seconds (8640.49 seconds total)