Starting phenix.real_space_refine on Tue Jul 29 21:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.map" model { file = "/net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xd1_33132/07_2025/7xd1_33132.cif" } resolution = 3.2 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 294 5.49 5 S 14 5.16 5 C 6648 2.51 5 N 2268 2.21 5 O 2824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 12048 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Time building chain proxies: 7.37, per 1000 atoms: 0.61 Number of scatterers: 12048 At special positions: 0 Unit cell: (119.214, 127.806, 91.29, 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 14 16.00 P 294 15.00 O 2824 8.00 N 2268 7.00 C 6648 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: 2.65 Conformation dependent library (CDL) restraints added in 882.3 milliseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 68.8% alpha, 3.2% beta 129 base pairs and 276 stacking pairs defined. Time for finding SS restraints: 6.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.927A pdb=" N TYR A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.525A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.847A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.581A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.132A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.637A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.641A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.737A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.535A pdb=" N ALA C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.646A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.639A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.588A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.565A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.845A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.999A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.749A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.641A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.737A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.535A pdb=" N ALA G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.646A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.639A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.572A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 84 removed outlier: 3.640A pdb=" N ARG D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.572A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 84 removed outlier: 3.640A pdb=" N ARG H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.580A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER H 112 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.907A 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: 6.597A 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: 7.291A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.013A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.220A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 343 hydrogen bonds defined for protein. 1017 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 317 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 276 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2152 1.33 - 1.45: 4325 1.45 - 1.57: 5772 1.57 - 1.69: 588 1.69 - 1.81: 24 Bond restraints: 12861 Sorted by residual: bond pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 1.520 1.598 -0.078 3.00e-02 1.11e+03 6.78e+00 bond pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sigma weight residual 1.520 1.597 -0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.42e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CG1 ILE B 50 " pdb=" CD1 ILE B 50 " ideal model delta sigma weight residual 1.513 1.435 0.078 3.90e-02 6.57e+02 4.04e+00 ... (remaining 12856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 18104 2.23 - 4.46: 478 4.46 - 6.70: 28 6.70 - 8.93: 12 8.93 - 11.16: 7 Bond angle restraints: 18629 Sorted by residual: angle pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " pdb=" CD GLU D 113 " ideal model delta sigma weight residual 112.60 123.17 -10.57 1.70e+00 3.46e-01 3.87e+01 angle pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " pdb=" CD GLU H 113 " ideal model delta sigma weight residual 112.60 123.16 -10.56 1.70e+00 3.46e-01 3.86e+01 angle pdb=" CA GLU H 113 " pdb=" CB GLU H 113 " pdb=" CG GLU H 113 " ideal model delta sigma weight residual 114.10 125.26 -11.16 2.00e+00 2.50e-01 3.11e+01 angle pdb=" CA GLU D 113 " pdb=" CB GLU D 113 " pdb=" CG GLU D 113 " ideal model delta sigma weight residual 114.10 125.19 -11.09 2.00e+00 2.50e-01 3.08e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 121.54 131.03 -9.49 1.91e+00 2.74e-01 2.47e+01 ... (remaining 18624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 5612 35.23 - 70.45: 1353 70.45 - 105.68: 8 105.68 - 140.90: 2 140.90 - 176.13: 2 Dihedral angle restraints: 6977 sinusoidal: 4775 harmonic: 2202 Sorted by residual: dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 153.63 26.37 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PRO E 121 " pdb=" C PRO E 121 " pdb=" N LYS E 122 " pdb=" CA LYS E 122 " ideal model delta harmonic sigma weight residual 180.00 158.63 21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual 180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 6974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1523 0.051 - 0.102: 513 0.102 - 0.153: 71 0.153 - 0.204: 9 0.204 - 0.255: 3 Chirality restraints: 2119 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" P DC I -58 " pdb=" OP1 DC I -58 " pdb=" OP2 DC I -58 " pdb=" O5' DC I -58 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2116 not shown) Planarity restraints: 1340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " 0.017 2.00e-02 2.50e+03 1.83e-02 6.68e+00 pdb=" CG TYR F 88 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " -0.016 2.00e-02 2.50e+03 1.54e-02 4.72e+00 pdb=" CG TYR B 51 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 25 " -0.012 2.00e-02 2.50e+03 1.46e-02 3.71e+00 pdb=" CG PHE C 25 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 25 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 25 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 25 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 25 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 25 " -0.003 2.00e-02 2.50e+03 ... (remaining 1337 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3453 2.85 - 3.37: 9714 3.37 - 3.88: 22898 3.88 - 4.39: 28712 4.39 - 4.90: 39523 Nonbonded interactions: 104300 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.343 3.040 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.344 3.040 nonbonded pdb=" NE2 GLN A 93 " pdb=" OE2 GLU A 97 " model vdw 2.345 3.120 nonbonded pdb=" O6 DG I -21 " pdb=" N4 DC J 21 " model vdw 2.381 3.120 nonbonded pdb=" O6 DG I -10 " pdb=" N4 DC J 10 " model vdw 2.391 3.120 ... (remaining 104295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.490 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.850 Find NCS groups from input model: 0.280 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.009 0.080 12861 Z= 0.378 Angle : 0.871 11.158 18629 Z= 0.501 Chirality : 0.049 0.255 2119 Planarity : 0.005 0.044 1340 Dihedral : 26.766 176.131 5557 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.59 % Allowed : 3.34 % Favored : 95.07 % 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: -5.83 (0.19), residues: 744 helix: -4.27 (0.11), residues: 524 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS C 82 PHE 0.033 0.004 PHE C 25 TYR 0.045 0.004 TYR F 88 ARG 0.014 0.002 ARG G 81 Details of bonding type rmsd hydrogen bonds : bond 0.30405 ( 660) hydrogen bonds : angle 10.15399 ( 1647) covalent geometry : bond 0.00890 (12861) covalent geometry : angle 0.87102 (18629) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 1.058 Fit side-chains REVERT: A 56 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7632 (ttpp) REVERT: A 107 THR cc_start: 0.9122 (t) cc_final: 0.8878 (p) REVERT: A 120 MET cc_start: 0.8199 (mtm) cc_final: 0.7969 (mtp) REVERT: B 93 GLN cc_start: 0.8220 (mt0) cc_final: 0.8005 (mt0) REVERT: C 50 TYR cc_start: 0.9089 (t80) cc_final: 0.8850 (t80) REVERT: C 76 THR cc_start: 0.8500 (p) cc_final: 0.8023 (t) REVERT: E 97 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7645 (mt-10) REVERT: G 75 LYS cc_start: 0.7932 (mttm) cc_final: 0.7661 (mtmt) REVERT: D 40 TYR cc_start: 0.8764 (m-80) cc_final: 0.7998 (m-80) REVERT: D 116 LYS cc_start: 0.8499 (ttpt) cc_final: 0.8288 (mtpt) REVERT: H 37 TYR cc_start: 0.8612 (m-80) cc_final: 0.8385 (m-80) REVERT: H 120 LYS cc_start: 0.7980 (tttp) cc_final: 0.7540 (ttmm) outliers start: 10 outliers final: 0 residues processed: 189 average time/residue: 0.3969 time to fit residues: 93.9061 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 104 GLN E 39 HIS E 108 ASN G 24 GLN G 82 HIS D 47 GLN H 95 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.147930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110556 restraints weight = 15829.278| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 0.86 r_work: 0.3051 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12861 Z= 0.178 Angle : 0.615 5.685 18629 Z= 0.370 Chirality : 0.037 0.155 2119 Planarity : 0.005 0.035 1340 Dihedral : 30.712 170.708 4059 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.27 % Allowed : 7.15 % Favored : 91.57 % 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: -2.50 (0.26), residues: 744 helix: -1.53 (0.19), residues: 538 sheet: None (None), residues: 0 loop : -1.49 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.010 0.002 PHE A 67 TYR 0.023 0.002 TYR B 51 ARG 0.003 0.000 ARG F 40 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 660) hydrogen bonds : angle 3.14833 ( 1647) covalent geometry : bond 0.00393 (12861) covalent geometry : angle 0.61505 (18629) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 153 time to evaluate : 0.871 Fit side-chains REVERT: A 56 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7987 (ttpp) REVERT: A 76 GLN cc_start: 0.7946 (mt0) cc_final: 0.7717 (mt0) REVERT: A 107 THR cc_start: 0.9239 (t) cc_final: 0.9016 (p) REVERT: A 120 MET cc_start: 0.8680 (mtm) cc_final: 0.8427 (mtp) REVERT: B 79 LYS cc_start: 0.8804 (mptt) cc_final: 0.8084 (mptt) REVERT: C 76 THR cc_start: 0.8720 (p) cc_final: 0.8439 (t) REVERT: E 90 MET cc_start: 0.7893 (mmp) cc_final: 0.7447 (mmp) REVERT: G 75 LYS cc_start: 0.7928 (mttm) cc_final: 0.7682 (mtmt) REVERT: D 36 SER cc_start: 0.9112 (p) cc_final: 0.8772 (p) REVERT: D 43 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8374 (mttt) REVERT: H 120 LYS cc_start: 0.8015 (tttp) cc_final: 0.7648 (ttmm) outliers start: 8 outliers final: 4 residues processed: 159 average time/residue: 0.4787 time to fit residues: 97.8600 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 134 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 109 HIS H 84 ASN H 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.104048 restraints weight = 16116.872| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 0.90 r_work: 0.2986 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12861 Z= 0.233 Angle : 0.635 5.803 18629 Z= 0.374 Chirality : 0.039 0.168 2119 Planarity : 0.006 0.043 1340 Dihedral : 30.948 170.127 4059 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.43 % Allowed : 10.02 % Favored : 88.55 % 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: -0.74 (0.29), residues: 744 helix: -0.10 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.19 (0.38), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 82 PHE 0.010 0.002 PHE A 67 TYR 0.020 0.002 TYR B 51 ARG 0.004 0.001 ARG B 45 Details of bonding type rmsd hydrogen bonds : bond 0.05272 ( 660) hydrogen bonds : angle 2.93718 ( 1647) covalent geometry : bond 0.00536 (12861) covalent geometry : angle 0.63476 (18629) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8297 (ttpt) cc_final: 0.8035 (ttpp) REVERT: A 76 GLN cc_start: 0.7979 (mt0) cc_final: 0.7774 (mt0) REVERT: A 107 THR cc_start: 0.9253 (t) cc_final: 0.9020 (p) REVERT: A 120 MET cc_start: 0.8606 (mtm) cc_final: 0.8377 (mtp) REVERT: B 79 LYS cc_start: 0.8829 (mptt) cc_final: 0.7994 (mptt) REVERT: C 76 THR cc_start: 0.8640 (p) cc_final: 0.8279 (t) REVERT: D 36 SER cc_start: 0.9124 (p) cc_final: 0.8825 (p) REVERT: D 43 LYS cc_start: 0.8699 (mtmm) cc_final: 0.8378 (mttt) outliers start: 9 outliers final: 6 residues processed: 140 average time/residue: 0.4268 time to fit residues: 76.3625 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.108304 restraints weight = 15858.183| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 0.85 r_work: 0.2978 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12861 Z= 0.188 Angle : 0.585 5.605 18629 Z= 0.351 Chirality : 0.036 0.155 2119 Planarity : 0.004 0.037 1340 Dihedral : 30.677 168.057 4059 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.75 % Allowed : 11.13 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.34 (0.30), residues: 744 helix: 0.74 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 109 PHE 0.008 0.001 PHE A 67 TYR 0.015 0.001 TYR B 51 ARG 0.004 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 660) hydrogen bonds : angle 2.72445 ( 1647) covalent geometry : bond 0.00426 (12861) covalent geometry : angle 0.58527 (18629) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.899 Fit side-chains REVERT: A 56 LYS cc_start: 0.8290 (ttpt) cc_final: 0.8006 (ttpp) REVERT: A 76 GLN cc_start: 0.8000 (mt0) cc_final: 0.7761 (mt0) REVERT: A 107 THR cc_start: 0.9212 (t) cc_final: 0.8973 (p) REVERT: A 120 MET cc_start: 0.8635 (mtm) cc_final: 0.8379 (mtp) REVERT: B 79 LYS cc_start: 0.8841 (mptt) cc_final: 0.8023 (mptt) REVERT: C 76 THR cc_start: 0.8575 (p) cc_final: 0.8313 (t) REVERT: E 90 MET cc_start: 0.7963 (mmp) cc_final: 0.7541 (mmp) REVERT: G 18 SER cc_start: 0.8978 (p) cc_final: 0.8745 (m) REVERT: D 36 SER cc_start: 0.9140 (p) cc_final: 0.8826 (p) REVERT: D 43 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8320 (mttt) outliers start: 11 outliers final: 10 residues processed: 136 average time/residue: 0.3529 time to fit residues: 62.1075 Evaluate side-chains 136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.142127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104263 restraints weight = 15930.841| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 0.91 r_work: 0.2996 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12861 Z= 0.192 Angle : 0.581 5.667 18629 Z= 0.348 Chirality : 0.037 0.156 2119 Planarity : 0.004 0.037 1340 Dihedral : 30.642 169.002 4059 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.07 % Allowed : 11.92 % Favored : 86.01 % 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: 0.84 (0.30), residues: 744 helix: 1.16 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 82 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.002 TYR B 51 ARG 0.004 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04653 ( 660) hydrogen bonds : angle 2.68371 ( 1647) covalent geometry : bond 0.00435 (12861) covalent geometry : angle 0.58127 (18629) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.836 Fit side-chains REVERT: A 56 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8097 (ttpp) REVERT: A 76 GLN cc_start: 0.8036 (mt0) cc_final: 0.7800 (mt0) REVERT: A 97 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: A 107 THR cc_start: 0.9198 (t) cc_final: 0.8963 (p) REVERT: A 120 MET cc_start: 0.8616 (mtm) cc_final: 0.8383 (mtp) REVERT: B 79 LYS cc_start: 0.8801 (mptt) cc_final: 0.7968 (mptt) REVERT: C 76 THR cc_start: 0.8589 (p) cc_final: 0.8252 (t) REVERT: E 90 MET cc_start: 0.8128 (mmp) cc_final: 0.7703 (mmp) REVERT: E 129 ARG cc_start: 0.8262 (tpt90) cc_final: 0.7603 (ttt90) REVERT: D 36 SER cc_start: 0.9131 (p) cc_final: 0.8789 (p) REVERT: D 43 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8304 (mttt) REVERT: H 120 LYS cc_start: 0.7984 (tttp) cc_final: 0.7594 (ttmm) outliers start: 13 outliers final: 9 residues processed: 135 average time/residue: 0.3638 time to fit residues: 63.1508 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103601 restraints weight = 16084.698| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 0.92 r_work: 0.2986 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12861 Z= 0.198 Angle : 0.582 5.678 18629 Z= 0.347 Chirality : 0.037 0.155 2119 Planarity : 0.004 0.038 1340 Dihedral : 30.622 168.379 4059 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.38 % Allowed : 11.76 % Favored : 85.85 % 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: 1.01 (0.30), residues: 744 helix: 1.31 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -0.88 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 660) hydrogen bonds : angle 2.68429 ( 1647) covalent geometry : bond 0.00451 (12861) covalent geometry : angle 0.58225 (18629) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.849 Fit side-chains REVERT: A 56 LYS cc_start: 0.8327 (ttpt) cc_final: 0.8068 (ttpp) REVERT: A 97 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: A 107 THR cc_start: 0.9232 (t) cc_final: 0.9015 (p) REVERT: A 120 MET cc_start: 0.8610 (mtm) cc_final: 0.8353 (mtp) REVERT: B 79 LYS cc_start: 0.8794 (mptt) cc_final: 0.7970 (mptt) REVERT: C 76 THR cc_start: 0.8551 (p) cc_final: 0.8302 (t) REVERT: E 90 MET cc_start: 0.8165 (mmp) cc_final: 0.7709 (mmp) REVERT: E 129 ARG cc_start: 0.8348 (tpt90) cc_final: 0.7650 (ttt90) REVERT: D 36 SER cc_start: 0.9110 (p) cc_final: 0.8790 (p) REVERT: D 43 LYS cc_start: 0.8592 (mtmm) cc_final: 0.8283 (mttt) REVERT: H 120 LYS cc_start: 0.7956 (tttp) cc_final: 0.7559 (ttmm) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.3375 time to fit residues: 60.6477 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.103347 restraints weight = 15965.820| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 0.93 r_work: 0.2985 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12861 Z= 0.188 Angle : 0.578 5.650 18629 Z= 0.345 Chirality : 0.037 0.185 2119 Planarity : 0.004 0.039 1340 Dihedral : 30.611 168.364 4059 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.54 % Allowed : 11.76 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.30), residues: 744 helix: 1.41 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.009 0.001 PHE F 100 TYR 0.012 0.001 TYR B 51 ARG 0.004 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04597 ( 660) hydrogen bonds : angle 2.67220 ( 1647) covalent geometry : bond 0.00426 (12861) covalent geometry : angle 0.57771 (18629) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.918 Fit side-chains REVERT: A 56 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8074 (ttpp) REVERT: A 97 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7766 (mt-10) REVERT: A 107 THR cc_start: 0.9229 (t) cc_final: 0.9007 (p) REVERT: A 120 MET cc_start: 0.8621 (mtm) cc_final: 0.8368 (mtp) REVERT: B 79 LYS cc_start: 0.8803 (mptt) cc_final: 0.7974 (mptt) REVERT: C 76 THR cc_start: 0.8576 (p) cc_final: 0.8300 (t) REVERT: E 90 MET cc_start: 0.8175 (mmp) cc_final: 0.7713 (mmp) REVERT: E 129 ARG cc_start: 0.8297 (tpt90) cc_final: 0.7609 (ttt90) REVERT: D 36 SER cc_start: 0.9111 (p) cc_final: 0.8804 (p) REVERT: D 43 LYS cc_start: 0.8575 (mtmm) cc_final: 0.8264 (mttt) REVERT: H 120 LYS cc_start: 0.7976 (tttp) cc_final: 0.7581 (ttmm) outliers start: 16 outliers final: 12 residues processed: 134 average time/residue: 0.3591 time to fit residues: 62.2329 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 15 optimal weight: 0.0010 overall best weight: 0.6966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104354 restraints weight = 16039.281| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 0.93 r_work: 0.3000 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12861 Z= 0.165 Angle : 0.569 5.524 18629 Z= 0.341 Chirality : 0.035 0.174 2119 Planarity : 0.004 0.039 1340 Dihedral : 30.603 168.252 4059 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.07 % Allowed : 12.72 % Favored : 85.21 % 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: 1.28 (0.31), residues: 744 helix: 1.50 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.008 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04509 ( 660) hydrogen bonds : angle 2.66343 ( 1647) covalent geometry : bond 0.00362 (12861) covalent geometry : angle 0.56875 (18629) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.917 Fit side-chains REVERT: A 56 LYS cc_start: 0.8331 (ttpt) cc_final: 0.8073 (ttpp) REVERT: A 97 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: A 107 THR cc_start: 0.9220 (t) cc_final: 0.9002 (p) REVERT: A 120 MET cc_start: 0.8617 (mtm) cc_final: 0.8364 (mtp) REVERT: B 79 LYS cc_start: 0.8792 (mptt) cc_final: 0.7962 (mptt) REVERT: C 76 THR cc_start: 0.8570 (p) cc_final: 0.8298 (t) REVERT: E 90 MET cc_start: 0.8155 (mmp) cc_final: 0.7699 (mmp) REVERT: E 129 ARG cc_start: 0.8310 (tpt90) cc_final: 0.7597 (ttt90) REVERT: D 36 SER cc_start: 0.9107 (p) cc_final: 0.8802 (p) REVERT: D 43 LYS cc_start: 0.8586 (mtmm) cc_final: 0.8268 (mttt) REVERT: H 120 LYS cc_start: 0.7975 (tttp) cc_final: 0.7579 (ttmm) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.3618 time to fit residues: 61.8675 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103452 restraints weight = 15974.139| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 0.95 r_work: 0.2990 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12861 Z= 0.183 Angle : 0.572 5.622 18629 Z= 0.343 Chirality : 0.036 0.171 2119 Planarity : 0.004 0.039 1340 Dihedral : 30.576 168.222 4059 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.38 % Allowed : 12.40 % Favored : 85.21 % 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: 1.34 (0.31), residues: 744 helix: 1.54 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -0.74 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.007 0.001 PHE A 67 TYR 0.013 0.001 TYR A 54 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04514 ( 660) hydrogen bonds : angle 2.65301 ( 1647) covalent geometry : bond 0.00412 (12861) covalent geometry : angle 0.57245 (18629) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.989 Fit side-chains REVERT: A 56 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8069 (ttpp) REVERT: A 97 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: A 107 THR cc_start: 0.9220 (t) cc_final: 0.8997 (p) REVERT: A 120 MET cc_start: 0.8636 (mtm) cc_final: 0.8383 (mtp) REVERT: B 79 LYS cc_start: 0.8748 (mptt) cc_final: 0.7891 (mptt) REVERT: C 76 THR cc_start: 0.8578 (p) cc_final: 0.8298 (t) REVERT: E 90 MET cc_start: 0.8177 (mmp) cc_final: 0.7720 (mmp) REVERT: E 129 ARG cc_start: 0.8320 (tpt90) cc_final: 0.7620 (ttt90) REVERT: D 36 SER cc_start: 0.9111 (p) cc_final: 0.8806 (p) REVERT: D 43 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8271 (mttt) REVERT: H 120 LYS cc_start: 0.7981 (tttp) cc_final: 0.7584 (ttmm) outliers start: 15 outliers final: 12 residues processed: 131 average time/residue: 0.3550 time to fit residues: 59.8233 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 55 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105084 restraints weight = 15900.242| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.92 r_work: 0.3031 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12861 Z= 0.152 Angle : 0.559 5.480 18629 Z= 0.337 Chirality : 0.035 0.166 2119 Planarity : 0.004 0.038 1340 Dihedral : 30.563 167.996 4059 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.91 % Allowed : 13.20 % Favored : 84.90 % 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: 1.49 (0.31), residues: 744 helix: 1.65 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -0.70 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 82 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR A 54 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 660) hydrogen bonds : angle 2.63781 ( 1647) covalent geometry : bond 0.00330 (12861) covalent geometry : angle 0.55853 (18629) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.863 Fit side-chains REVERT: A 56 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8066 (ttpp) REVERT: A 97 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 107 THR cc_start: 0.9203 (t) cc_final: 0.8987 (p) REVERT: A 120 MET cc_start: 0.8582 (mtm) cc_final: 0.8334 (mtp) REVERT: B 79 LYS cc_start: 0.8736 (mptt) cc_final: 0.7887 (mptt) REVERT: C 76 THR cc_start: 0.8568 (p) cc_final: 0.8296 (t) REVERT: E 90 MET cc_start: 0.8127 (mmp) cc_final: 0.7676 (mmp) REVERT: E 129 ARG cc_start: 0.8298 (tpt90) cc_final: 0.7626 (ttt90) REVERT: G 18 SER cc_start: 0.9014 (p) cc_final: 0.8771 (m) REVERT: D 36 SER cc_start: 0.9097 (p) cc_final: 0.8797 (p) REVERT: D 43 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8268 (mttt) REVERT: H 120 LYS cc_start: 0.7982 (tttp) cc_final: 0.7605 (ttmm) outliers start: 12 outliers final: 11 residues processed: 129 average time/residue: 0.3601 time to fit residues: 59.8638 Evaluate side-chains 134 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain E residue 49 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.141638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103401 restraints weight = 15888.909| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 0.93 r_work: 0.2995 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12861 Z= 0.188 Angle : 0.573 5.658 18629 Z= 0.343 Chirality : 0.036 0.168 2119 Planarity : 0.004 0.037 1340 Dihedral : 30.535 168.423 4059 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.23 % Allowed : 12.72 % Favored : 85.06 % 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: 1.47 (0.31), residues: 744 helix: 1.64 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -0.71 (0.39), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 49 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.003 0.000 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 660) hydrogen bonds : angle 2.64736 ( 1647) covalent geometry : bond 0.00426 (12861) covalent geometry : angle 0.57301 (18629) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6183.68 seconds wall clock time: 109 minutes 40.84 seconds (6580.84 seconds total)