Starting phenix.real_space_refine on Thu Jan 23 05:24:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gd0_51238/01_2025/9gd0_51238.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gd0_51238/01_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_51238/01_2025/9gd0_51238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gd0_51238/01_2025/9gd0_51238.map" model { file = "/net/cci-nas-00/data/ceres_data/9gd0_51238/01_2025/9gd0_51238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gd0_51238/01_2025/9gd0_51238.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 11.41, per 1000 atoms: 0.56 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: 4.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 11.13 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: 11.19 Time building geometry restraints manager: 5.80 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: 0.010 Normalize map: mean=0, sd=1: 2.930 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: 0.060 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 54.950 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.640 ------------------------------------------------------------------------------- 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= 0.305 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.013 0.002 HIS F 75 PHE 0.016 0.003 PHE D 67 TYR 0.027 0.005 TYR M 57 ARG 0.017 0.003 ARG A 63 *********************** 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 : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7508 (tt0) cc_final: 0.7251 (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: 0.8429 (t) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 2.0124 time to fit residues: 657.0920 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 : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.0470 chunk 128 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 106 HIS E 93 GLN M 24 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.115476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.086190 restraints weight = 45601.040| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.54 r_work: 0.3261 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1877 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= 0.228 Angle : 0.620 7.802 31309 Z= 0.380 Chirality : 0.034 0.146 3578 Planarity : 0.004 0.039 2225 Dihedral : 30.504 72.916 6859 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.15 % Allowed : 12.77 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1225 helix: 1.58 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.02 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 75 PHE 0.010 0.001 PHE K 67 TYR 0.012 0.002 TYR B 51 ARG 0.009 0.001 ARG O 72 *********************** 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 278 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 ARG cc_start: 0.8897 (ttm-80) cc_final: 0.8594 (ttm110) REVERT: C 61 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: D 54 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8269 (mtmm) REVERT: D 110 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: D 113 LYS cc_start: 0.9017 (tttt) cc_final: 0.8787 (tttm) REVERT: G 41 GLU cc_start: 0.8274 (pm20) cc_final: 0.7503 (pm20) REVERT: H 43 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8231 (mmpt) REVERT: K 79 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8105 (tmtt) REVERT: M 61 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8394 (tp30) REVERT: M 73 ASN cc_start: 0.8627 (t0) cc_final: 0.8276 (t0) REVERT: M 95 LYS cc_start: 0.9075 (ttmp) cc_final: 0.8772 (tppp) REVERT: O 90 MET cc_start: 0.8411 (mtp) cc_final: 0.8130 (mtp) outliers start: 33 outliers final: 7 residues processed: 254 average time/residue: 2.0344 time to fit residues: 562.2470 Evaluate side-chains 230 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 218 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 114 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 110 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 82 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 64 LYS 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 39 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 98 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN B 93 GLN D 106 HIS ** 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 = 0.3980 r_free = 0.3980 target = 0.114483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085217 restraints weight = 45243.297| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.54 r_work: 0.3238 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21584 Z= 0.221 Angle : 0.569 8.197 31309 Z= 0.347 Chirality : 0.033 0.151 3578 Planarity : 0.004 0.042 2225 Dihedral : 30.178 71.024 6859 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 3.15 % Allowed : 14.49 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.23), residues: 1225 helix: 2.11 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.07 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.009 0.001 PHE K 67 TYR 0.015 0.002 TYR B 88 ARG 0.008 0.001 ARG B 35 *********************** 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: 33 poor density : 238 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8646 (mtp85) REVERT: C 61 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: C 64 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: D 110 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: D 118 TYR cc_start: 0.9251 (t80) cc_final: 0.9029 (t80) REVERT: F 92 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8218 (ttm-80) REVERT: K 76 GLN cc_start: 0.8406 (pt0) cc_final: 0.7925 (pt0) REVERT: K 79 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8377 (tmtt) REVERT: M 73 ASN cc_start: 0.8651 (t0) cc_final: 0.8239 (t0) REVERT: M 95 LYS cc_start: 0.9104 (ttmp) cc_final: 0.8809 (tppp) REVERT: O 90 MET cc_start: 0.8435 (mtp) cc_final: 0.8005 (mtp) REVERT: P 95 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (ptp90) outliers start: 33 outliers final: 13 residues processed: 248 average time/residue: 1.9863 time to fit residues: 535.3029 Evaluate side-chains 237 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 92 ARG 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 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 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 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 95 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 101 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 58 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN D 46 HIS D 106 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.080510 restraints weight = 45435.960| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.58 r_work: 0.3141 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 21584 Z= 0.428 Angle : 0.660 8.844 31309 Z= 0.392 Chirality : 0.040 0.155 3578 Planarity : 0.005 0.037 2225 Dihedral : 30.714 72.688 6859 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.72 % Allowed : 15.82 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.23), residues: 1225 helix: 1.74 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.28 (0.33), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS M 31 PHE 0.015 0.002 PHE K 67 TYR 0.018 0.002 TYR B 88 ARG 0.009 0.001 ARG B 35 *********************** 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 272 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9166 (t80) cc_final: 0.8432 (t80) REVERT: C 61 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7930 (mp0) REVERT: C 64 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: C 75 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8412 (mmtt) REVERT: D 118 TYR cc_start: 0.9309 (t80) cc_final: 0.9024 (t80) REVERT: F 92 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8384 (ttm-80) REVERT: F 93 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: G 41 GLU cc_start: 0.8290 (pm20) cc_final: 0.7873 (pm20) REVERT: H 43 LYS cc_start: 0.8916 (ttmm) cc_final: 0.8675 (tppt) REVERT: H 44 GLN cc_start: 0.8968 (tt0) cc_final: 0.8754 (mt0) REVERT: K 73 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7138 (mm-30) REVERT: K 76 GLN cc_start: 0.8540 (pt0) cc_final: 0.7908 (pt0) REVERT: K 79 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.7711 (tmtt) REVERT: M 73 ASN cc_start: 0.8818 (t0) cc_final: 0.8373 (t0) REVERT: O 90 MET cc_start: 0.8429 (mtp) cc_final: 0.7491 (mtp) REVERT: O 94 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7784 (mp0) outliers start: 39 outliers final: 19 residues processed: 244 average time/residue: 1.9883 time to fit residues: 528.8006 Evaluate side-chains 240 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 215 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 72 ASP 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 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 82 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 79 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 16 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS G 104 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083327 restraints weight = 45630.192| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.54 r_work: 0.3200 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21584 Z= 0.238 Angle : 0.577 9.184 31309 Z= 0.350 Chirality : 0.034 0.154 3578 Planarity : 0.004 0.042 2225 Dihedral : 30.130 70.770 6859 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.86 % Allowed : 17.06 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.23), residues: 1225 helix: 2.12 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 75 PHE 0.010 0.001 PHE A 67 TYR 0.018 0.002 TYR N 80 ARG 0.008 0.001 ARG P 78 *********************** 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 263 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 1.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9154 (t80) cc_final: 0.8180 (t80) REVERT: C 61 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: C 64 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: C 75 LYS cc_start: 0.8867 (mmtp) cc_final: 0.8450 (mmtt) REVERT: C 102 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.8934 (mt) REVERT: D 118 TYR cc_start: 0.9255 (t80) cc_final: 0.8984 (t80) REVERT: F 92 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8412 (ttm-80) REVERT: F 93 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7404 (mp10) REVERT: G 41 GLU cc_start: 0.8218 (pm20) cc_final: 0.7896 (pm20) REVERT: H 73 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: K 73 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6972 (mm-30) REVERT: K 76 GLN cc_start: 0.8446 (pt0) cc_final: 0.7781 (pt0) REVERT: M 73 ASN cc_start: 0.8657 (t0) cc_final: 0.8177 (t0) REVERT: M 90 ASP cc_start: 0.8282 (t0) cc_final: 0.8036 (t0) REVERT: O 90 MET cc_start: 0.8325 (mtp) cc_final: 0.7429 (mtp) REVERT: O 94 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7630 (mp0) outliers start: 30 outliers final: 12 residues processed: 241 average time/residue: 1.9434 time to fit residues: 509.3584 Evaluate side-chains 242 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 101 THR 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 54 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 84 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 100 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 9 optimal weight: 0.0270 chunk 118 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4020 ------------------------------------------------------------------------------- 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 ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082459 restraints weight = 45329.189| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.56 r_work: 0.3181 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21584 Z= 0.274 Angle : 0.595 9.552 31309 Z= 0.358 Chirality : 0.035 0.155 3578 Planarity : 0.004 0.040 2225 Dihedral : 30.221 70.474 6859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.76 % Allowed : 17.73 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.23), residues: 1225 helix: 2.15 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.25 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE K 67 TYR 0.018 0.002 TYR B 88 ARG 0.009 0.001 ARG P 78 *********************** 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 260 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9172 (t80) cc_final: 0.8216 (t80) REVERT: C 61 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: C 64 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: C 102 ILE cc_start: 0.9492 (OUTLIER) cc_final: 0.8949 (mt) REVERT: D 54 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8144 (mptt) REVERT: E 133 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7685 (mt-10) REVERT: F 92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8424 (ttm-80) REVERT: F 93 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: G 41 GLU cc_start: 0.8152 (pm20) cc_final: 0.7925 (pm20) REVERT: H 43 LYS cc_start: 0.8863 (tppt) cc_final: 0.8494 (mmtm) REVERT: H 73 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8187 (tm-30) REVERT: K 73 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7045 (mm-30) REVERT: K 76 GLN cc_start: 0.8449 (pt0) cc_final: 0.7784 (pt0) REVERT: M 73 ASN cc_start: 0.8672 (t0) cc_final: 0.8316 (t0) REVERT: O 90 MET cc_start: 0.8314 (mtp) cc_final: 0.7434 (mtp) REVERT: O 94 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7671 (mp0) outliers start: 29 outliers final: 15 residues processed: 241 average time/residue: 1.9581 time to fit residues: 512.6742 Evaluate side-chains 245 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 223 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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 101 THR 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 55 LEU 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 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 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 91 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 164 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 106 HIS G 104 GLN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 ASN ** 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 = 0.3955 r_free = 0.3955 target = 0.112733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083492 restraints weight = 45314.945| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.53 r_work: 0.3207 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3436 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= 0.205 Angle : 0.589 9.804 31309 Z= 0.354 Chirality : 0.034 0.160 3578 Planarity : 0.004 0.060 2225 Dihedral : 30.190 70.410 6859 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.57 % Allowed : 18.11 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.23), residues: 1225 helix: 2.27 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 106 PHE 0.010 0.001 PHE K 67 TYR 0.021 0.002 TYR B 88 ARG 0.010 0.001 ARG P 78 *********************** 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 261 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9161 (t80) cc_final: 0.8180 (t80) REVERT: C 61 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 64 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8214 (tp30) REVERT: C 102 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.8941 (mt) REVERT: D 54 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8119 (mptt) REVERT: E 133 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 91 LYS cc_start: 0.9154 (ttpt) cc_final: 0.8928 (tttt) REVERT: F 92 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.8415 (ttm-80) REVERT: F 93 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: H 43 LYS cc_start: 0.8838 (tppt) cc_final: 0.8436 (mmtm) REVERT: H 73 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8151 (tm-30) REVERT: K 73 GLU cc_start: 0.7372 (mm-30) cc_final: 0.7107 (mm-30) REVERT: K 76 GLN cc_start: 0.8388 (pt0) cc_final: 0.7867 (pt0) REVERT: K 79 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8441 (tptp) REVERT: K 133 GLU cc_start: 0.6308 (OUTLIER) cc_final: 0.5495 (mp0) REVERT: M 73 ASN cc_start: 0.8580 (t0) cc_final: 0.8329 (t0) REVERT: M 90 ASP cc_start: 0.8252 (t0) cc_final: 0.8039 (t0) REVERT: O 90 MET cc_start: 0.8287 (mtp) cc_final: 0.7399 (mtp) REVERT: O 94 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: P 78 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.8121 (mtm110) outliers start: 27 outliers final: 15 residues processed: 243 average time/residue: 1.9650 time to fit residues: 519.4711 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 : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR 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 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 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 N residue 84 SER 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 161 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.081655 restraints weight = 45648.024| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.53 r_work: 0.3174 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 21584 Z= 0.318 Angle : 0.618 10.347 31309 Z= 0.368 Chirality : 0.037 0.151 3578 Planarity : 0.005 0.041 2225 Dihedral : 30.289 70.534 6859 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.76 % Allowed : 18.40 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.23), residues: 1225 helix: 2.11 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.26 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS M 31 PHE 0.013 0.002 PHE K 67 TYR 0.029 0.002 TYR B 88 ARG 0.010 0.001 ARG B 35 *********************** 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 257 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 57 TYR cc_start: 0.9171 (t80) cc_final: 0.8212 (t80) REVERT: C 61 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 64 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8250 (tp30) REVERT: C 102 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.8951 (mt) REVERT: D 54 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8115 (mptt) REVERT: D 73 GLU cc_start: 0.9158 (tp30) cc_final: 0.8956 (mm-30) REVERT: D 110 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: F 92 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8454 (ttm-80) REVERT: F 93 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: H 43 LYS cc_start: 0.8896 (tppt) cc_final: 0.8500 (mmtm) REVERT: H 65 ASP cc_start: 0.9214 (t0) cc_final: 0.9004 (t0) REVERT: H 73 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: K 73 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7045 (mm-30) REVERT: K 76 GLN cc_start: 0.8444 (pt0) cc_final: 0.7927 (pt0) REVERT: M 73 ASN cc_start: 0.8746 (t0) cc_final: 0.8315 (t0) REVERT: O 90 MET cc_start: 0.8383 (mtp) cc_final: 0.7521 (mtp) REVERT: O 94 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7718 (mp0) outliers start: 29 outliers final: 15 residues processed: 237 average time/residue: 1.9721 time to fit residues: 508.7765 Evaluate side-chains 245 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 222 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR 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 54 LYS Chi-restraints excluded: chain H residue 73 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 80 THR 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 60 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 106 HIS G 104 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.112005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.082566 restraints weight = 45361.829| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.54 r_work: 0.3185 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21584 Z= 0.238 Angle : 0.620 11.338 31309 Z= 0.368 Chirality : 0.035 0.155 3578 Planarity : 0.005 0.072 2225 Dihedral : 30.303 70.394 6859 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.23), residues: 1225 helix: 2.18 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.23 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS N 46 PHE 0.013 0.001 PHE K 67 TYR 0.047 0.002 TYR B 88 ARG 0.014 0.001 ARG P 78 *********************** 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 259 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 64 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8216 (tp30) REVERT: C 102 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.8945 (mt) REVERT: D 54 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8124 (mptt) REVERT: D 110 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: F 92 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8431 (ttm-80) REVERT: F 93 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7413 (mp10) REVERT: G 41 GLU cc_start: 0.8204 (pm20) cc_final: 0.7651 (pm20) REVERT: H 43 LYS cc_start: 0.8900 (tppt) cc_final: 0.8508 (mmtm) REVERT: H 65 ASP cc_start: 0.9167 (t0) cc_final: 0.8965 (t0) REVERT: H 73 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: K 73 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7008 (mm-30) REVERT: K 76 GLN cc_start: 0.8403 (pt0) cc_final: 0.7937 (pt0) REVERT: K 79 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8403 (tptp) REVERT: O 90 MET cc_start: 0.8316 (mtp) cc_final: 0.7403 (mtp) REVERT: O 94 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7649 (mp0) outliers start: 32 outliers final: 18 residues processed: 238 average time/residue: 1.9692 time to fit residues: 510.6307 Evaluate side-chains 247 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR 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 86 SER 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 44 GLN 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 65 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 106 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS G 104 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.112097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082597 restraints weight = 45548.781| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.54 r_work: 0.3184 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21584 Z= 0.259 Angle : 0.611 11.288 31309 Z= 0.364 Chirality : 0.035 0.153 3578 Planarity : 0.005 0.072 2225 Dihedral : 30.256 71.137 6859 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.23), residues: 1225 helix: 2.20 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.22 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 106 PHE 0.012 0.001 PHE K 67 TYR 0.040 0.002 TYR B 88 ARG 0.014 0.001 ARG P 78 ********************** 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 250 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: C 64 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: C 102 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.8938 (mt) REVERT: D 54 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8125 (mptt) REVERT: D 110 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: F 92 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8397 (ttm-80) REVERT: F 93 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: G 41 GLU cc_start: 0.8215 (pm20) cc_final: 0.7820 (pm20) REVERT: H 43 LYS cc_start: 0.8899 (tppt) cc_final: 0.8513 (mmtm) REVERT: H 65 ASP cc_start: 0.9171 (t0) cc_final: 0.8962 (t0) REVERT: H 73 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: K 73 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7024 (mm-30) REVERT: K 76 GLN cc_start: 0.8400 (pt0) cc_final: 0.7920 (pt0) REVERT: O 90 MET cc_start: 0.8289 (mtp) cc_final: 0.7399 (mtp) REVERT: O 94 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: P 78 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8239 (mtm110) outliers start: 26 outliers final: 17 residues processed: 232 average time/residue: 1.9581 time to fit residues: 493.8477 Evaluate side-chains 246 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR 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 86 SER 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 44 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 118 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 106 HIS G 104 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.112388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082926 restraints weight = 45631.845| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.56 r_work: 0.3187 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21584 Z= 0.222 Angle : 0.608 11.239 31309 Z= 0.362 Chirality : 0.034 0.151 3578 Planarity : 0.005 0.065 2225 Dihedral : 30.253 71.673 6859 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.96 % Allowed : 18.78 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.23), residues: 1225 helix: 2.24 (0.16), residues: 940 sheet: None (None), residues: 0 loop : -0.19 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 106 PHE 0.012 0.001 PHE K 67 TYR 0.042 0.002 TYR B 88 ARG 0.011 0.001 ARG P 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17805.18 seconds wall clock time: 313 minutes 0.20 seconds (18780.20 seconds total)