Starting phenix.real_space_refine on Mon Jul 28 23:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.cif Found real_map, /net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.map" model { file = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8whb_37538/07_2025/8whb_37538.cif" } resolution = 3.17 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= 0.000 sd= 0.003 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 268 5.49 5 S 12 5.16 5 C 6211 2.51 5 N 2067 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11176 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 733 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 799 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 621 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "G" Number of atoms: 700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 700 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "H" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 716 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "I" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2729 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Chain: "J" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2765 Classifications: {'DNA': 134} Link IDs: {'rna3p': 133} Time building chain proxies: 7.83, per 1000 atoms: 0.70 Number of scatterers: 11176 At special positions: 0 Unit cell: (118.845, 101.745, 127.395, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 268 15.00 O 2618 8.00 N 2067 7.00 C 6211 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: 3.02 Conformation dependent library (CDL) restraints added in 1.1 seconds 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1352 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 74.4% alpha, 3.3% beta 86 base pairs and 224 stacking pairs defined. Time for finding SS restraints: 6.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.668A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.639A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.747A 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 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.697A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.909A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 removed outlier: 3.966A pdb=" N LEU C 117 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 Processing helix chain 'D' and resid 80 through 109 removed outlier: 3.736A pdb=" N ASN D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 127 removed outlier: 3.732A pdb=" N ILE D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 removed outlier: 3.743A pdb=" N SER D 137 " --> pdb=" O LYS D 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.606A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.586A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.791A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR E 99 " --> pdb=" O ALA E 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 130 removed outlier: 3.804A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.871A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.689A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.452A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU G 59 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 removed outlier: 3.602A pdb=" N ASP G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 80 through 109 removed outlier: 3.786A pdb=" N ASN H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 127 removed outlier: 3.879A pdb=" N THR H 121 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 148 removed outlier: 3.667A pdb=" N ALA H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.960A pdb=" N ARG A 83 " --> pdb=" O VAL F 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 45 through 46 removed outlier: 7.545A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 7.000A pdb=" N THR B 96 " --> pdb=" O THR C 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.449A pdb=" N ARG C 43 " --> pdb=" O ILE D 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98 removed outlier: 6.609A pdb=" N THR F 96 " --> pdb=" O THR G 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.158A pdb=" N ARG G 43 " --> pdb=" O ILE H 114 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 359 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 224 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1313 1.32 - 1.44: 4203 1.44 - 1.56: 5846 1.56 - 1.68: 537 1.68 - 1.80: 22 Bond restraints: 11921 Sorted by residual: bond pdb=" N GLU F 52 " pdb=" CA GLU F 52 " ideal model delta sigma weight residual 1.455 1.504 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" NE ARG C 89 " pdb=" CZ ARG C 89 " ideal model delta sigma weight residual 1.326 1.365 -0.039 1.10e-02 8.26e+03 1.27e+01 bond pdb=" N ILE F 26 " pdb=" CA ILE F 26 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N GLN F 27 " pdb=" CA GLN F 27 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.35e-02 5.49e+03 1.02e+01 bond pdb=" N LYS F 59 " pdb=" CA LYS F 59 " ideal model delta sigma weight residual 1.459 1.499 -0.041 1.28e-02 6.10e+03 1.01e+01 ... (remaining 11916 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 16857 2.80 - 5.59: 352 5.59 - 8.39: 31 8.39 - 11.19: 2 11.19 - 13.98: 5 Bond angle restraints: 17247 Sorted by residual: angle pdb=" O3' DT J 9 " pdb=" C3' DT J 9 " pdb=" C2' DT J 9 " ideal model delta sigma weight residual 111.50 125.48 -13.98 1.50e+00 4.44e-01 8.69e+01 angle pdb=" N THR E 107 " pdb=" CA THR E 107 " pdb=" C THR E 107 " ideal model delta sigma weight residual 113.18 102.29 10.89 1.21e+00 6.83e-01 8.10e+01 angle pdb=" O3' DA I 106 " pdb=" C3' DA I 106 " pdb=" C2' DA I 106 " ideal model delta sigma weight residual 111.50 124.99 -13.49 1.50e+00 4.44e-01 8.09e+01 angle pdb=" O3' DG I 126 " pdb=" C3' DG I 126 " pdb=" C2' DG I 126 " ideal model delta sigma weight residual 111.50 124.43 -12.93 1.50e+00 4.44e-01 7.43e+01 angle pdb=" O3' DT J 24 " pdb=" C3' DT J 24 " pdb=" C2' DT J 24 " ideal model delta sigma weight residual 111.50 124.43 -12.93 1.50e+00 4.44e-01 7.43e+01 ... (remaining 17242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.91: 5232 34.91 - 69.82: 1200 69.82 - 104.74: 34 104.74 - 139.65: 2 139.65 - 174.56: 4 Dihedral angle restraints: 6472 sinusoidal: 4381 harmonic: 2091 Sorted by residual: dihedral pdb=" CA GLU H 118 " pdb=" C GLU H 118 " pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta harmonic sigma weight residual 180.00 152.95 27.05 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -157.21 -22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU E 133 " pdb=" C GLU E 133 " pdb=" N ARG E 134 " pdb=" CA ARG E 134 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1955 0.164 - 0.329: 12 0.329 - 0.493: 0 0.493 - 0.657: 2 0.657 - 0.821: 3 Chirality restraints: 1972 Sorted by residual: chirality pdb=" C3' DG I 126 " pdb=" C4' DG I 126 " pdb=" O3' DG I 126 " pdb=" C2' DG I 126 " both_signs ideal model delta sigma weight residual False -2.66 -1.84 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C3' DA I 106 " pdb=" C4' DA I 106 " pdb=" O3' DA I 106 " pdb=" C2' DA I 106 " both_signs ideal model delta sigma weight residual False -2.66 -1.94 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C3' DT J 24 " pdb=" C4' DT J 24 " pdb=" O3' DT J 24 " pdb=" C2' DT J 24 " both_signs ideal model delta sigma weight residual False -2.66 -1.98 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 1969 not shown) Planarity restraints: 1249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.045 2.00e-02 2.50e+03 2.09e-02 9.82e+00 pdb=" N1 DC J 27 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " 0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.025 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 106 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C ASP E 106 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP E 106 " -0.019 2.00e-02 2.50e+03 pdb=" N THR E 107 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR F 51 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.01e+00 pdb=" C TYR F 51 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR F 51 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 52 " -0.018 2.00e-02 2.50e+03 ... (remaining 1246 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2427 2.80 - 3.32: 9588 3.32 - 3.85: 20983 3.85 - 4.37: 25240 4.37 - 4.90: 35944 Nonbonded interactions: 94182 Sorted by model distance: nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR G 58 " pdb=" OE2 GLU G 62 " model vdw 2.335 3.040 nonbonded pdb=" NE ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.342 3.120 nonbonded pdb=" OH TYR C 40 " pdb=" OE1 GLU D 96 " model vdw 2.415 3.040 nonbonded pdb=" NH2 ARG E 131 " pdb=" OE2 GLU E 133 " model vdw 2.420 3.120 ... (remaining 94177 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' and resid 43 through 133) } ncs_group { reference = (chain 'B' and resid 24 through 100) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 18 through 110) selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 61 through 149) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.530 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:3.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.007 0.059 11921 Z= 0.356 Angle : 1.006 13.981 17247 Z= 0.640 Chirality : 0.060 0.821 1972 Planarity : 0.006 0.055 1249 Dihedral : 27.902 174.559 5120 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -2.07 (0.29), residues: 707 helix: -0.87 (0.22), residues: 510 sheet: None (None), residues: 0 loop : -2.40 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 83 PHE 0.049 0.003 PHE C 26 TYR 0.013 0.003 TYR H 65 ARG 0.010 0.001 ARG G 89 Details of bonding type rmsd hydrogen bonds : bond 0.20894 ( 575) hydrogen bonds : angle 7.77230 ( 1488) covalent geometry : bond 0.00740 (11921) covalent geometry : angle 1.00567 (17247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.831 Fit side-chains REVERT: C 105 ASN cc_start: 0.8857 (t0) cc_final: 0.8656 (t0) REVERT: C 111 ASN cc_start: 0.8084 (t0) cc_final: 0.7741 (p0) REVERT: D 111 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8191 (mtpt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.4103 time to fit residues: 101.8223 Evaluate side-chains 152 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 85 GLN H 74 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.128163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.092685 restraints weight = 20881.797| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.55 r_work: 0.3098 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11921 Z= 0.178 Angle : 0.626 8.805 17247 Z= 0.370 Chirality : 0.037 0.258 1972 Planarity : 0.005 0.045 1249 Dihedral : 30.961 176.787 3713 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.68 % Allowed : 10.74 % Favored : 87.58 % 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: 0.19 (0.32), residues: 707 helix: 0.88 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -2.01 (0.40), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.010 0.001 PHE B 61 TYR 0.008 0.001 TYR F 51 ARG 0.007 0.001 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.05130 ( 575) hydrogen bonds : angle 3.08309 ( 1488) covalent geometry : bond 0.00383 (11921) covalent geometry : angle 0.62631 (17247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 1.004 Fit side-chains REVERT: B 84 MET cc_start: 0.8308 (mmm) cc_final: 0.8007 (mmt) REVERT: C 18 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.7892 (mpp80) REVERT: C 74 ASN cc_start: 0.7122 (m-40) cc_final: 0.6561 (t0) REVERT: C 89 ARG cc_start: 0.8790 (mmt90) cc_final: 0.8575 (mmt180) REVERT: C 105 ASN cc_start: 0.9015 (t0) cc_final: 0.8214 (t0) REVERT: C 111 ASN cc_start: 0.8377 (t0) cc_final: 0.7872 (p0) REVERT: D 111 LYS cc_start: 0.8480 (mmtm) cc_final: 0.8175 (mtpt) REVERT: D 141 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (ttpp) REVERT: F 79 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8802 (mtmt) REVERT: H 104 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8028 (ttmm) outliers start: 10 outliers final: 2 residues processed: 170 average time/residue: 0.4680 time to fit residues: 99.5062 Evaluate side-chains 161 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 157 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain E residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 24 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.085159 restraints weight = 20648.408| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.51 r_work: 0.2965 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11921 Z= 0.170 Angle : 0.574 6.963 17247 Z= 0.341 Chirality : 0.035 0.141 1972 Planarity : 0.004 0.042 1249 Dihedral : 30.836 178.266 3713 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.01 % Allowed : 13.42 % Favored : 84.56 % 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: 1.30 (0.32), residues: 707 helix: 1.68 (0.23), residues: 524 sheet: None (None), residues: 0 loop : -1.61 (0.42), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.019 0.001 PHE C 26 TYR 0.008 0.001 TYR B 51 ARG 0.005 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.04989 ( 575) hydrogen bonds : angle 2.78206 ( 1488) covalent geometry : bond 0.00368 (11921) covalent geometry : angle 0.57392 (17247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.843 Fit side-chains REVERT: C 18 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8154 (mpp80) REVERT: C 74 ASN cc_start: 0.7438 (m-40) cc_final: 0.6958 (t0) REVERT: C 78 ARG cc_start: 0.8941 (mtm-85) cc_final: 0.8604 (mtm-85) REVERT: C 105 ASN cc_start: 0.8933 (t0) cc_final: 0.8149 (t0) REVERT: C 111 ASN cc_start: 0.8410 (t0) cc_final: 0.7965 (p0) REVERT: D 104 LYS cc_start: 0.8273 (mptt) cc_final: 0.7956 (mtmm) REVERT: D 111 LYS cc_start: 0.8614 (mmtm) cc_final: 0.8211 (mtpt) REVERT: F 79 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8831 (mtmt) REVERT: H 104 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8362 (ttmm) outliers start: 12 outliers final: 6 residues processed: 176 average time/residue: 0.3960 time to fit residues: 86.5604 Evaluate side-chains 161 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 69 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 75 HIS H 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.109685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.072482 restraints weight = 20505.057| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.68 r_work: 0.2691 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11921 Z= 0.256 Angle : 0.644 8.670 17247 Z= 0.377 Chirality : 0.040 0.167 1972 Planarity : 0.005 0.040 1249 Dihedral : 30.921 177.360 3713 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.52 % Allowed : 12.58 % 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 (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: 1.35 (0.32), residues: 707 helix: 1.75 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.63 (0.41), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.022 0.002 PHE C 26 TYR 0.012 0.001 TYR B 51 ARG 0.006 0.001 ARG G 78 Details of bonding type rmsd hydrogen bonds : bond 0.06449 ( 575) hydrogen bonds : angle 3.05912 ( 1488) covalent geometry : bond 0.00595 (11921) covalent geometry : angle 0.64441 (17247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 165 time to evaluate : 0.855 Fit side-chains REVERT: A 79 LYS cc_start: 0.8988 (tttm) cc_final: 0.8757 (tttt) REVERT: C 18 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.8292 (mpp80) REVERT: C 73 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: C 74 ASN cc_start: 0.8370 (m-40) cc_final: 0.7821 (t0) REVERT: C 105 ASN cc_start: 0.9057 (t0) cc_final: 0.8386 (t0) REVERT: C 111 ASN cc_start: 0.8479 (t0) cc_final: 0.8177 (p0) REVERT: D 82 LYS cc_start: 0.8983 (mttt) cc_final: 0.8763 (mttm) REVERT: D 104 LYS cc_start: 0.8305 (mptt) cc_final: 0.8039 (mtmm) REVERT: D 111 LYS cc_start: 0.8858 (mmtm) cc_final: 0.8481 (mtpt) REVERT: F 79 LYS cc_start: 0.9127 (mtpt) cc_final: 0.8782 (mtmt) REVERT: H 68 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8887 (mttt) REVERT: H 130 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7659 (tm-30) outliers start: 21 outliers final: 11 residues processed: 172 average time/residue: 0.3945 time to fit residues: 84.3536 Evaluate side-chains 166 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 7 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN E 68 GLN F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.078288 restraints weight = 20664.685| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.62 r_work: 0.2812 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11921 Z= 0.150 Angle : 0.535 7.075 17247 Z= 0.320 Chirality : 0.033 0.125 1972 Planarity : 0.004 0.038 1249 Dihedral : 30.469 178.299 3713 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.52 % Allowed : 13.59 % 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 (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: 1.99 (0.33), residues: 707 helix: 2.28 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.60 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.006 0.001 TYR H 65 ARG 0.005 0.000 ARG D 124 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 575) hydrogen bonds : angle 2.56443 ( 1488) covalent geometry : bond 0.00324 (11921) covalent geometry : angle 0.53464 (17247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.817 Fit side-chains REVERT: C 18 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8329 (mpp80) REVERT: C 73 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.8088 (m-30) REVERT: C 74 ASN cc_start: 0.7736 (m-40) cc_final: 0.7291 (t0) REVERT: C 105 ASN cc_start: 0.9075 (t0) cc_final: 0.8288 (t0) REVERT: C 109 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7990 (mtm) REVERT: D 104 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7890 (mtmm) REVERT: D 111 LYS cc_start: 0.8651 (mmtm) cc_final: 0.8226 (mtpt) REVERT: F 67 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8378 (ttp80) REVERT: H 68 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8882 (mttt) REVERT: H 130 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7551 (tm-30) outliers start: 15 outliers final: 9 residues processed: 169 average time/residue: 0.3910 time to fit residues: 82.2241 Evaluate side-chains 170 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.111169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.074476 restraints weight = 20764.255| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.66 r_work: 0.2728 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11921 Z= 0.190 Angle : 0.563 7.798 17247 Z= 0.334 Chirality : 0.035 0.147 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.512 177.775 3713 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.68 % Allowed : 15.77 % Favored : 82.55 % 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: 2.13 (0.33), residues: 707 helix: 2.34 (0.23), residues: 523 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 113 PHE 0.016 0.001 PHE C 26 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.05149 ( 575) hydrogen bonds : angle 2.70583 ( 1488) covalent geometry : bond 0.00430 (11921) covalent geometry : angle 0.56252 (17247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.794 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8269 (mpp80) REVERT: C 73 ASP cc_start: 0.8460 (m-30) cc_final: 0.8187 (m-30) REVERT: C 74 ASN cc_start: 0.8028 (m-40) cc_final: 0.7596 (t0) REVERT: C 105 ASN cc_start: 0.9066 (t0) cc_final: 0.8253 (t0) REVERT: C 109 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: D 104 LYS cc_start: 0.8262 (mptt) cc_final: 0.8051 (mtmm) REVERT: D 111 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8334 (mtpt) REVERT: H 68 LYS cc_start: 0.9192 (ttmt) cc_final: 0.8899 (mttt) REVERT: H 130 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7648 (tm-30) outliers start: 10 outliers final: 5 residues processed: 162 average time/residue: 0.4371 time to fit residues: 88.8293 Evaluate side-chains 165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.0040 chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.111783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075185 restraints weight = 20866.254| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.67 r_work: 0.2744 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11921 Z= 0.159 Angle : 0.547 7.242 17247 Z= 0.327 Chirality : 0.034 0.150 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.476 177.974 3713 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.17 % Allowed : 16.61 % Favored : 82.21 % 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: 2.16 (0.33), residues: 707 helix: 2.36 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.48 (0.42), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 113 PHE 0.014 0.001 PHE C 26 TYR 0.008 0.001 TYR B 51 ARG 0.003 0.000 ARG G 33 Details of bonding type rmsd hydrogen bonds : bond 0.04831 ( 575) hydrogen bonds : angle 2.65369 ( 1488) covalent geometry : bond 0.00346 (11921) covalent geometry : angle 0.54747 (17247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8318 (mpp80) REVERT: C 73 ASP cc_start: 0.8450 (m-30) cc_final: 0.8181 (m-30) REVERT: C 74 ASN cc_start: 0.7989 (m-40) cc_final: 0.7552 (t0) REVERT: C 105 ASN cc_start: 0.9068 (t0) cc_final: 0.8247 (t0) REVERT: C 109 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7999 (mtm) REVERT: D 104 LYS cc_start: 0.8233 (mptt) cc_final: 0.8006 (mtmm) REVERT: D 111 LYS cc_start: 0.8682 (mmtm) cc_final: 0.8335 (mtpt) REVERT: F 79 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8906 (mtmm) REVERT: H 68 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8887 (mttt) REVERT: H 130 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7645 (tm-30) outliers start: 7 outliers final: 5 residues processed: 161 average time/residue: 0.4550 time to fit residues: 91.9898 Evaluate side-chains 165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.109355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074122 restraints weight = 20517.620| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.52 r_work: 0.2746 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.5983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11921 Z= 0.264 Angle : 0.628 8.579 17247 Z= 0.368 Chirality : 0.039 0.176 1972 Planarity : 0.004 0.035 1249 Dihedral : 30.550 177.999 3713 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.85 % Allowed : 15.94 % Favored : 82.21 % 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: 1.80 (0.32), residues: 707 helix: 2.13 (0.23), residues: 519 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 113 PHE 0.018 0.002 PHE C 26 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.001 ARG G 33 Details of bonding type rmsd hydrogen bonds : bond 0.06414 ( 575) hydrogen bonds : angle 2.94991 ( 1488) covalent geometry : bond 0.00617 (11921) covalent geometry : angle 0.62824 (17247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.877 Fit side-chains REVERT: C 18 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8289 (mtp85) REVERT: C 73 ASP cc_start: 0.8750 (m-30) cc_final: 0.8480 (m-30) REVERT: C 74 ASN cc_start: 0.8547 (m-40) cc_final: 0.8064 (t0) REVERT: C 105 ASN cc_start: 0.9159 (t0) cc_final: 0.8392 (t0) REVERT: C 109 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: D 104 LYS cc_start: 0.8497 (mptt) cc_final: 0.8253 (mtmm) REVERT: D 111 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8626 (mtpt) REVERT: G 89 ARG cc_start: 0.8651 (mmt180) cc_final: 0.8342 (mmt180) REVERT: H 68 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8930 (mttt) REVERT: H 130 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8046 (tm-30) outliers start: 11 outliers final: 7 residues processed: 165 average time/residue: 0.5354 time to fit residues: 109.6871 Evaluate side-chains 165 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.077619 restraints weight = 20581.846| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.50 r_work: 0.2823 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11921 Z= 0.159 Angle : 0.562 7.219 17247 Z= 0.334 Chirality : 0.034 0.147 1972 Planarity : 0.004 0.047 1249 Dihedral : 30.369 178.137 3713 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.01 % Allowed : 15.60 % Favored : 82.38 % 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: 2.13 (0.33), residues: 707 helix: 2.36 (0.23), residues: 518 sheet: None (None), residues: 0 loop : -1.42 (0.42), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.026 0.001 PHE A 67 TYR 0.007 0.001 TYR B 51 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04818 ( 575) hydrogen bonds : angle 2.69629 ( 1488) covalent geometry : bond 0.00346 (11921) covalent geometry : angle 0.56188 (17247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 158 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: C 18 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8299 (mpp80) REVERT: C 73 ASP cc_start: 0.8660 (m-30) cc_final: 0.8419 (m-30) REVERT: C 74 ASN cc_start: 0.8391 (m-40) cc_final: 0.7931 (t0) REVERT: C 105 ASN cc_start: 0.9162 (t0) cc_final: 0.8382 (t0) REVERT: C 109 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: D 104 LYS cc_start: 0.8354 (mptt) cc_final: 0.8123 (mtmm) REVERT: D 111 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8508 (mtpt) REVERT: H 68 LYS cc_start: 0.9194 (ttmt) cc_final: 0.8900 (mttt) REVERT: H 104 LYS cc_start: 0.8751 (ttmm) cc_final: 0.8407 (ttmm) REVERT: H 130 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7939 (tm-30) outliers start: 12 outliers final: 7 residues processed: 162 average time/residue: 0.4298 time to fit residues: 87.8175 Evaluate side-chains 163 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 75 optimal weight: 5.9990 chunk 45 optimal weight: 0.0020 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.111951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.076224 restraints weight = 20535.542| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.48 r_work: 0.2781 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11921 Z= 0.154 Angle : 0.541 7.153 17247 Z= 0.322 Chirality : 0.033 0.157 1972 Planarity : 0.004 0.036 1249 Dihedral : 30.228 178.409 3713 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 15.77 % Favored : 82.38 % 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 (0.33), residues: 707 helix: 2.56 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.010 0.001 PHE A 67 TYR 0.009 0.001 TYR B 88 ARG 0.005 0.000 ARG B 23 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 575) hydrogen bonds : angle 2.59152 ( 1488) covalent geometry : bond 0.00337 (11921) covalent geometry : angle 0.54126 (17247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1414 Ramachandran restraints generated. 707 Oldfield, 0 Emsley, 707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8516 (m-30) cc_final: 0.8293 (m-30) REVERT: C 74 ASN cc_start: 0.8069 (m-40) cc_final: 0.7608 (t0) REVERT: C 105 ASN cc_start: 0.9139 (t0) cc_final: 0.8319 (t0) REVERT: D 111 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8321 (mtpt) REVERT: H 63 LYS cc_start: 0.9057 (mptt) cc_final: 0.8778 (mmtp) REVERT: H 68 LYS cc_start: 0.9214 (ttmt) cc_final: 0.8913 (mttt) REVERT: H 84 MET cc_start: 0.9002 (tpp) cc_final: 0.8629 (mmt) REVERT: H 130 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7821 (tm-30) outliers start: 11 outliers final: 7 residues processed: 159 average time/residue: 0.4055 time to fit residues: 80.4910 Evaluate side-chains 156 residues out of total 596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 149 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain G residue 102 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.111727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.076839 restraints weight = 20554.055| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.51 r_work: 0.2812 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.6237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11921 Z= 0.197 Angle : 0.566 7.136 17247 Z= 0.333 Chirality : 0.035 0.159 1972 Planarity : 0.004 0.065 1249 Dihedral : 30.276 178.267 3713 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.17 % Allowed : 16.28 % Favored : 82.55 % 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: 2.36 (0.33), residues: 707 helix: 2.51 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 74 PHE 0.021 0.002 PHE A 67 TYR 0.009 0.001 TYR B 51 ARG 0.006 0.000 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.05147 ( 575) hydrogen bonds : angle 2.68613 ( 1488) covalent geometry : bond 0.00450 (11921) covalent geometry : angle 0.56557 (17247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7521.30 seconds wall clock time: 139 minutes 12.09 seconds (8352.09 seconds total)