Starting phenix.real_space_refine on Tue May 13 09:03:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0f_62699/05_2025/9l0f_62699.cif" } resolution = 4.1 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6300 2.51 5 N 1596 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9954 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "H" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "J" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "K" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Chain: "L" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1659 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 9, 'TRANS': 207} Time building chain proxies: 6.37, per 1000 atoms: 0.64 Number of scatterers: 9954 At special positions: 0 Unit cell: (129.2, 142.8, 65.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 2010 8.00 N 1596 7.00 C 6300 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 26 sheets defined 5.5% alpha, 49.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'G' and resid 150 through 161 removed outlier: 3.819A pdb=" N ILE G 154 " --> pdb=" O PRO G 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 161 removed outlier: 3.876A pdb=" N ILE H 154 " --> pdb=" O PRO H 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 161 removed outlier: 3.865A pdb=" N ILE I 154 " --> pdb=" O PRO I 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 161 removed outlier: 3.900A pdb=" N ILE J 154 " --> pdb=" O PRO J 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 161 removed outlier: 3.821A pdb=" N ILE K 154 " --> pdb=" O PRO K 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 161 removed outlier: 3.873A pdb=" N ILE L 154 " --> pdb=" O PRO L 150 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 60 through 62 removed outlier: 5.149A pdb=" N TYR G 45 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER G 91 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET G 90 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU G 20 " --> pdb=" O MET G 90 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE G 92 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLU G 18 " --> pdb=" O PHE G 92 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS G 94 " --> pdb=" O GLY G 16 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER G 14 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP G 98 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLU G 12 " --> pdb=" O TRP G 98 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU G 100 " --> pdb=" O PHE G 10 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE G 10 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA G 166 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLN G 193 " --> pdb=" O GLU G 196 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU G 198 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER G 191 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 104 through 111 removed outlier: 7.640A pdb=" N VAL G 104 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA G 144 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU G 106 " --> pdb=" O THR G 142 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL G 137 " --> pdb=" O LEU G 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'G' and resid 114 through 119 removed outlier: 3.979A pdb=" N PHE G 133 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TYR G 117 " --> pdb=" O PRO G 131 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR G 119 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLN G 129 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 98 through 100 removed outlier: 3.512A pdb=" N GLN H 8 " --> pdb=" O TYR H 170 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA H 166 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN H 193 " --> pdb=" O GLU H 196 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLU H 198 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER H 191 " --> pdb=" O GLU H 198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 104 through 111 removed outlier: 7.721A pdb=" N VAL H 104 " --> pdb=" O ALA H 144 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ALA H 144 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 106 " --> pdb=" O THR H 142 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N VAL H 137 " --> pdb=" O LEU H 206 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 19 through 21 removed outlier: 6.977A pdb=" N SER H 91 " --> pdb=" O THR H 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 23 through 24 removed outlier: 4.197A pdb=" N ALA H 23 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 114 through 119 removed outlier: 3.988A pdb=" N PHE H 133 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR H 117 " --> pdb=" O PRO H 131 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR H 119 " --> pdb=" O GLN H 129 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLN H 129 " --> pdb=" O TYR H 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 60 through 62 removed outlier: 5.141A pdb=" N TYR I 45 " --> pdb=" O ILE I 95 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER I 91 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET I 90 " --> pdb=" O ALA I 21 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS I 94 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL I 17 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR I 96 " --> pdb=" O ARG I 15 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ARG I 15 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TRP I 98 " --> pdb=" O THR I 13 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 13 " --> pdb=" O TRP I 98 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N GLU I 100 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL I 11 " --> pdb=" O GLU I 100 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN I 8 " --> pdb=" O TYR I 170 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA I 166 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N MET I 197 " --> pdb=" O GLN I 193 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLN I 193 " --> pdb=" O MET I 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR I 199 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 104 through 111 removed outlier: 7.573A pdb=" N VAL I 104 " --> pdb=" O ALA I 144 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ALA I 144 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU I 106 " --> pdb=" O THR I 142 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL I 137 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE I 213 " --> pdb=" O MET I 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 31 through 33 Processing sheet with id=AB4, first strand: chain 'I' and resid 114 through 119 removed outlier: 3.899A pdb=" N PHE I 133 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR I 117 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N TYR I 119 " --> pdb=" O GLN I 129 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLN I 129 " --> pdb=" O TYR I 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 98 through 100 removed outlier: 3.508A pdb=" N GLN J 8 " --> pdb=" O TYR J 170 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA J 166 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN J 193 " --> pdb=" O GLU J 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU J 198 " --> pdb=" O SER J 191 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER J 191 " --> pdb=" O GLU J 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 104 through 111 removed outlier: 7.714A pdb=" N VAL J 104 " --> pdb=" O ALA J 144 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ALA J 144 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU J 106 " --> pdb=" O THR J 142 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL J 137 " --> pdb=" O LEU J 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 19 through 21 removed outlier: 3.521A pdb=" N MET J 90 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N SER J 91 " --> pdb=" O THR J 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 23 through 24 removed outlier: 4.132A pdb=" N ALA J 23 " --> pdb=" O THR J 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 114 through 119 removed outlier: 3.963A pdb=" N PHE J 133 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR J 117 " --> pdb=" O PRO J 131 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR J 119 " --> pdb=" O GLN J 129 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLN J 129 " --> pdb=" O TYR J 119 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 60 through 62 removed outlier: 5.138A pdb=" N TYR K 45 " --> pdb=" O ILE K 95 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER K 91 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET K 90 " --> pdb=" O GLU K 20 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLU K 20 " --> pdb=" O MET K 90 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N PHE K 92 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLU K 18 " --> pdb=" O PHE K 92 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS K 94 " --> pdb=" O GLY K 16 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER K 14 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP K 98 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLU K 12 " --> pdb=" O TRP K 98 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU K 100 " --> pdb=" O PHE K 10 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE K 10 " --> pdb=" O GLU K 100 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA K 166 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N MET K 197 " --> pdb=" O GLN K 193 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN K 193 " --> pdb=" O MET K 197 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR K 199 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 104 through 111 removed outlier: 6.878A pdb=" N THR K 142 " --> pdb=" O GLN K 105 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE K 107 " --> pdb=" O THR K 140 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR K 140 " --> pdb=" O ILE K 107 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN K 109 " --> pdb=" O SER K 138 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER K 138 " --> pdb=" O GLN K 109 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N VAL K 137 " --> pdb=" O LEU K 206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 31 through 32 Processing sheet with id=AC4, first strand: chain 'K' and resid 114 through 119 removed outlier: 3.979A pdb=" N PHE K 133 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N TYR K 117 " --> pdb=" O PRO K 131 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR K 119 " --> pdb=" O GLN K 129 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N GLN K 129 " --> pdb=" O TYR K 119 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 60 through 62 removed outlier: 5.168A pdb=" N TYR L 45 " --> pdb=" O ILE L 95 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER L 91 " --> pdb=" O THR L 49 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS L 94 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL L 17 " --> pdb=" O LYS L 94 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR L 96 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ARG L 15 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N TRP L 98 " --> pdb=" O THR L 13 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR L 13 " --> pdb=" O TRP L 98 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU L 100 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL L 11 " --> pdb=" O GLU L 100 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN L 8 " --> pdb=" O TYR L 170 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ALA L 166 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N MET L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLN L 193 " --> pdb=" O MET L 197 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR L 199 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 104 through 111 removed outlier: 7.581A pdb=" N VAL L 104 " --> pdb=" O ALA L 144 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA L 144 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU L 106 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL L 137 " --> pdb=" O LEU L 206 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET L 177 " --> pdb=" O ILE L 213 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 213 " --> pdb=" O MET L 177 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 31 through 33 Processing sheet with id=AC8, first strand: chain 'L' and resid 114 through 119 removed outlier: 3.903A pdb=" N PHE L 133 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR L 117 " --> pdb=" O PRO L 131 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR L 119 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N GLN L 129 " --> pdb=" O TYR L 119 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.79 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3240 1.34 - 1.46: 1990 1.46 - 1.57: 4826 1.57 - 1.69: 6 1.69 - 1.81: 84 Bond restraints: 10146 Sorted by residual: bond pdb=" CA ASN J 26 " pdb=" CB ASN J 26 " ideal model delta sigma weight residual 1.528 1.592 -0.064 2.61e-02 1.47e+03 5.99e+00 bond pdb=" CA ASN H 26 " pdb=" CB ASN H 26 " ideal model delta sigma weight residual 1.536 1.601 -0.065 4.10e-02 5.95e+02 2.48e+00 bond pdb=" CA ASN G 26 " pdb=" CB ASN G 26 " ideal model delta sigma weight residual 1.536 1.592 -0.056 4.10e-02 5.95e+02 1.83e+00 bond pdb=" CA ASN K 26 " pdb=" CB ASN K 26 " ideal model delta sigma weight residual 1.536 1.591 -0.055 4.10e-02 5.95e+02 1.79e+00 bond pdb=" N GLY I 208 " pdb=" CA GLY I 208 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.35e+00 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 13277 1.42 - 2.84: 464 2.84 - 4.26: 68 4.26 - 5.68: 7 5.68 - 7.10: 8 Bond angle restraints: 13824 Sorted by residual: angle pdb=" N ILE L 76 " pdb=" CA ILE L 76 " pdb=" C ILE L 76 " ideal model delta sigma weight residual 112.12 109.20 2.92 8.40e-01 1.42e+00 1.21e+01 angle pdb=" CA MET H 56 " pdb=" CB MET H 56 " pdb=" CG MET H 56 " ideal model delta sigma weight residual 114.10 120.39 -6.29 2.00e+00 2.50e-01 9.88e+00 angle pdb=" CA MET L 56 " pdb=" CB MET L 56 " pdb=" CG MET L 56 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.70e+00 angle pdb=" CA MET I 56 " pdb=" CB MET I 56 " pdb=" CG MET I 56 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.33e+00 angle pdb=" N ILE I 76 " pdb=" CA ILE I 76 " pdb=" C ILE I 76 " ideal model delta sigma weight residual 112.12 109.93 2.19 8.40e-01 1.42e+00 6.83e+00 ... (remaining 13819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 5357 17.67 - 35.34: 539 35.34 - 53.01: 108 53.01 - 70.68: 31 70.68 - 88.35: 19 Dihedral angle restraints: 6054 sinusoidal: 2280 harmonic: 3774 Sorted by residual: dihedral pdb=" CB GLU J 198 " pdb=" CG GLU J 198 " pdb=" CD GLU J 198 " pdb=" OE1 GLU J 198 " ideal model delta sinusoidal sigma weight residual 0.00 -88.35 88.35 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU H 198 " pdb=" CG GLU H 198 " pdb=" CD GLU H 198 " pdb=" OE1 GLU H 198 " ideal model delta sinusoidal sigma weight residual 0.00 -87.34 87.34 1 3.00e+01 1.11e-03 1.02e+01 dihedral pdb=" CG ARG K 59 " pdb=" CD ARG K 59 " pdb=" NE ARG K 59 " pdb=" CZ ARG K 59 " ideal model delta sinusoidal sigma weight residual -90.00 -131.70 41.70 2 1.50e+01 4.44e-03 9.44e+00 ... (remaining 6051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 910 0.028 - 0.055: 393 0.055 - 0.083: 133 0.083 - 0.110: 137 0.110 - 0.138: 65 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA ILE G 101 " pdb=" N ILE G 101 " pdb=" C ILE G 101 " pdb=" CB ILE G 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA ASP H 188 " pdb=" N ASP H 188 " pdb=" C ASP H 188 " pdb=" CB ASP H 188 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE K 101 " pdb=" N ILE K 101 " pdb=" C ILE K 101 " pdb=" CB ILE K 101 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1635 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP K 39 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.84e+00 pdb=" C ASP K 39 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP K 39 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU K 40 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 69 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C THR J 69 " 0.028 2.00e-02 2.50e+03 pdb=" O THR J 69 " -0.010 2.00e-02 2.50e+03 pdb=" N SER J 70 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 147 " -0.012 2.00e-02 2.50e+03 1.21e-02 2.58e+00 pdb=" CG PHE J 147 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE J 147 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE J 147 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE J 147 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE J 147 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 147 " -0.001 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3469 2.85 - 3.36: 8429 3.36 - 3.87: 14663 3.87 - 4.39: 15986 4.39 - 4.90: 29511 Nonbonded interactions: 72058 Sorted by model distance: nonbonded pdb=" NE2 HIS G 2 " pdb=" OE1 GLU H 198 " model vdw 2.336 3.120 nonbonded pdb=" OE1 GLU J 198 " pdb=" NE2 HIS K 2 " model vdw 2.352 3.120 nonbonded pdb=" OD2 ASP J 44 " pdb=" NZ LYS J 94 " model vdw 2.376 3.120 nonbonded pdb=" O TRP J 53 " pdb=" N LYS J 55 " model vdw 2.391 3.120 nonbonded pdb=" N ASP K 77 " pdb=" OD1 ASP K 77 " model vdw 2.404 3.120 ... (remaining 72053 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: 0.02 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 1.050 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.950 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.004 0.065 10146 Z= 0.161 Angle : 0.615 7.099 13824 Z= 0.353 Chirality : 0.048 0.138 1638 Planarity : 0.004 0.038 1770 Dihedral : 15.815 88.353 3618 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.12 % Favored : 93.57 % Rotamer: Outliers : 0.36 % Allowed : 17.84 % Favored : 81.79 % 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 (0.22), residues: 1290 helix: 1.91 (0.64), residues: 66 sheet: 0.46 (0.25), residues: 426 loop : -1.44 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 180 HIS 0.001 0.000 HIS L 145 PHE 0.028 0.002 PHE J 147 TYR 0.013 0.001 TYR G 170 ARG 0.004 0.001 ARG H 178 Details of bonding type rmsd hydrogen bonds : bond 0.23485 ( 311) hydrogen bonds : angle 7.93948 ( 903) covalent geometry : bond 0.00354 (10146) covalent geometry : angle 0.61454 (13824) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 1.119 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 69 average time/residue: 0.3004 time to fit residues: 27.7794 Evaluate side-chains 38 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.025289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2197 r_free = 0.2197 target = 0.019913 restraints weight = 94051.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2228 r_free = 0.2228 target = 0.020707 restraints weight = 51112.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2251 r_free = 0.2251 target = 0.021281 restraints weight = 33693.551| |-----------------------------------------------------------------------------| r_work (final): 0.2247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10146 Z= 0.142 Angle : 0.544 5.485 13824 Z= 0.290 Chirality : 0.048 0.149 1638 Planarity : 0.004 0.034 1770 Dihedral : 3.909 16.085 1368 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.12 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % 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: -0.96 (0.23), residues: 1290 helix: 1.65 (0.60), residues: 72 sheet: -0.09 (0.23), residues: 540 loop : -1.37 (0.21), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 53 HIS 0.001 0.001 HIS I 145 PHE 0.014 0.002 PHE J 84 TYR 0.010 0.001 TYR K 170 ARG 0.003 0.000 ARG L 168 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 311) hydrogen bonds : angle 5.40544 ( 903) covalent geometry : bond 0.00324 (10146) covalent geometry : angle 0.54384 (13824) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9513 (ptp) cc_final: 0.9256 (ppp) REVERT: G 90 MET cc_start: 0.9767 (ttt) cc_final: 0.9090 (tmm) REVERT: G 207 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9285 (mmmm) REVERT: H 56 MET cc_start: 0.9607 (ptp) cc_final: 0.9157 (pmm) REVERT: H 90 MET cc_start: 0.9488 (ttm) cc_final: 0.8901 (tmm) REVERT: H 177 MET cc_start: 0.8420 (tpp) cc_final: 0.8125 (tpt) REVERT: I 56 MET cc_start: 0.9363 (ptp) cc_final: 0.8743 (pmm) REVERT: J 56 MET cc_start: 0.9618 (ptp) cc_final: 0.9347 (pmm) REVERT: J 90 MET cc_start: 0.9458 (ttm) cc_final: 0.8864 (tmm) REVERT: J 177 MET cc_start: 0.8458 (tpp) cc_final: 0.8225 (tpt) REVERT: J 207 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8585 (mptt) REVERT: K 56 MET cc_start: 0.9513 (ptp) cc_final: 0.9252 (ppp) REVERT: K 90 MET cc_start: 0.9760 (ttt) cc_final: 0.9061 (tmm) REVERT: L 56 MET cc_start: 0.9345 (ptp) cc_final: 0.8902 (pmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3308 time to fit residues: 23.7535 Evaluate side-chains 42 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 70 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 10 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 overall best weight: 3.1984 ------------------------------------------------------------------------------- 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 = 0.2418 r_free = 0.2418 target = 0.024808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2182 r_free = 0.2182 target = 0.019533 restraints weight = 95085.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2213 r_free = 0.2213 target = 0.020309 restraints weight = 51019.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2235 r_free = 0.2235 target = 0.020864 restraints weight = 33357.622| |-----------------------------------------------------------------------------| r_work (final): 0.2231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10146 Z= 0.114 Angle : 0.499 5.933 13824 Z= 0.266 Chirality : 0.047 0.140 1638 Planarity : 0.004 0.032 1770 Dihedral : 3.723 15.326 1368 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.97 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -0.99 (0.23), residues: 1290 helix: 1.54 (0.58), residues: 72 sheet: -0.33 (0.22), residues: 594 loop : -1.19 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 53 HIS 0.001 0.000 HIS G 145 PHE 0.013 0.001 PHE J 84 TYR 0.005 0.001 TYR K 170 ARG 0.004 0.001 ARG L 178 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 311) hydrogen bonds : angle 4.98843 ( 903) covalent geometry : bond 0.00264 (10146) covalent geometry : angle 0.49882 (13824) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9589 (ptp) cc_final: 0.9261 (ppp) REVERT: G 90 MET cc_start: 0.9774 (ttt) cc_final: 0.9189 (tmm) REVERT: G 177 MET cc_start: 0.8816 (mmm) cc_final: 0.8537 (mmm) REVERT: G 207 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9288 (mmmm) REVERT: H 56 MET cc_start: 0.9659 (ptp) cc_final: 0.9264 (pmm) REVERT: H 177 MET cc_start: 0.8403 (tpp) cc_final: 0.8188 (tpp) REVERT: I 56 MET cc_start: 0.9396 (ptp) cc_final: 0.8718 (pmm) REVERT: I 169 MET cc_start: 0.9466 (ttm) cc_final: 0.9191 (ttm) REVERT: I 177 MET cc_start: 0.8719 (tpt) cc_final: 0.7978 (tpt) REVERT: J 56 MET cc_start: 0.9687 (ptp) cc_final: 0.8911 (pmm) REVERT: J 90 MET cc_start: 0.9487 (ttm) cc_final: 0.8842 (tmm) REVERT: J 177 MET cc_start: 0.8331 (tpp) cc_final: 0.7873 (tpt) REVERT: K 56 MET cc_start: 0.9611 (ptp) cc_final: 0.9287 (ppp) REVERT: K 90 MET cc_start: 0.9759 (ttt) cc_final: 0.9174 (tmm) REVERT: K 177 MET cc_start: 0.9043 (mmm) cc_final: 0.8725 (mmm) REVERT: L 177 MET cc_start: 0.8550 (tpt) cc_final: 0.8214 (tpt) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3559 time to fit residues: 25.1951 Evaluate side-chains 40 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 114 GLN H 114 GLN I 114 GLN L 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2331 r_free = 0.2331 target = 0.022674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2094 r_free = 0.2094 target = 0.017722 restraints weight = 101362.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2125 r_free = 0.2125 target = 0.018440 restraints weight = 54461.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2147 r_free = 0.2147 target = 0.018945 restraints weight = 35645.189| |-----------------------------------------------------------------------------| r_work (final): 0.2138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10146 Z= 0.207 Angle : 0.541 4.998 13824 Z= 0.291 Chirality : 0.047 0.139 1638 Planarity : 0.004 0.030 1770 Dihedral : 4.114 16.452 1368 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -1.10 (0.23), residues: 1290 helix: 1.97 (0.58), residues: 72 sheet: -0.50 (0.22), residues: 582 loop : -1.21 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 53 HIS 0.003 0.001 HIS G 145 PHE 0.014 0.002 PHE K 147 TYR 0.008 0.001 TYR K 170 ARG 0.014 0.001 ARG H 59 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 311) hydrogen bonds : angle 4.96864 ( 903) covalent geometry : bond 0.00458 (10146) covalent geometry : angle 0.54116 (13824) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9622 (ptp) cc_final: 0.9226 (ppp) REVERT: G 90 MET cc_start: 0.9797 (ttt) cc_final: 0.9318 (tmm) REVERT: G 207 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9301 (mmmm) REVERT: H 56 MET cc_start: 0.9468 (ptp) cc_final: 0.9248 (pmm) REVERT: I 56 MET cc_start: 0.9476 (ptp) cc_final: 0.8812 (pmm) REVERT: I 90 MET cc_start: 0.9328 (ttm) cc_final: 0.9097 (ttm) REVERT: I 169 MET cc_start: 0.9685 (ttm) cc_final: 0.9396 (ttp) REVERT: J 56 MET cc_start: 0.9623 (ptp) cc_final: 0.9321 (pmm) REVERT: K 56 MET cc_start: 0.9623 (ptp) cc_final: 0.9240 (ppp) REVERT: K 90 MET cc_start: 0.9801 (ttt) cc_final: 0.9262 (tmm) REVERT: L 177 MET cc_start: 0.8650 (tpt) cc_final: 0.8197 (tpt) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.3160 time to fit residues: 21.9251 Evaluate side-chains 42 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 2 HIS G 163 GLN K 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2368 r_free = 0.2368 target = 0.023151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2132 r_free = 0.2132 target = 0.018158 restraints weight = 99053.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2164 r_free = 0.2164 target = 0.018900 restraints weight = 53266.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2187 r_free = 0.2187 target = 0.019430 restraints weight = 34757.341| |-----------------------------------------------------------------------------| r_work (final): 0.2180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10146 Z= 0.113 Angle : 0.492 9.170 13824 Z= 0.261 Chirality : 0.047 0.140 1638 Planarity : 0.004 0.031 1770 Dihedral : 3.816 15.877 1368 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.12 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: -0.97 (0.23), residues: 1290 helix: 1.94 (0.57), residues: 72 sheet: -0.37 (0.21), residues: 582 loop : -1.16 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 53 HIS 0.001 0.000 HIS G 145 PHE 0.009 0.001 PHE L 212 TYR 0.012 0.001 TYR G 170 ARG 0.003 0.000 ARG K 178 Details of bonding type rmsd hydrogen bonds : bond 0.02819 ( 311) hydrogen bonds : angle 4.60511 ( 903) covalent geometry : bond 0.00259 (10146) covalent geometry : angle 0.49241 (13824) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9581 (ptp) cc_final: 0.9356 (ppp) REVERT: G 90 MET cc_start: 0.9796 (ttt) cc_final: 0.9313 (tpt) REVERT: H 56 MET cc_start: 0.9571 (ptp) cc_final: 0.8935 (ppp) REVERT: H 173 LYS cc_start: 0.9622 (mmtt) cc_final: 0.9388 (tptp) REVERT: I 56 MET cc_start: 0.9394 (ptp) cc_final: 0.8772 (pmm) REVERT: I 90 MET cc_start: 0.9276 (ttm) cc_final: 0.9044 (ttm) REVERT: I 177 MET cc_start: 0.8675 (tpt) cc_final: 0.8436 (tpt) REVERT: J 56 MET cc_start: 0.9624 (ptp) cc_final: 0.9337 (pmm) REVERT: K 56 MET cc_start: 0.9582 (ptp) cc_final: 0.9279 (ppp) REVERT: K 90 MET cc_start: 0.9792 (ttt) cc_final: 0.9315 (tpt) REVERT: K 207 LYS cc_start: 0.9433 (mmmm) cc_final: 0.8868 (mmtm) REVERT: L 169 MET cc_start: 0.9635 (ttp) cc_final: 0.9214 (ptt) REVERT: L 177 MET cc_start: 0.8617 (tpt) cc_final: 0.8091 (tpt) REVERT: L 207 LYS cc_start: 0.9359 (mmmm) cc_final: 0.8819 (mmtm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3204 time to fit residues: 22.4758 Evaluate side-chains 43 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 89 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 16 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 2 HIS K 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2321 r_free = 0.2321 target = 0.022203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2083 r_free = 0.2083 target = 0.017316 restraints weight = 101546.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2114 r_free = 0.2114 target = 0.018020 restraints weight = 54409.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2137 r_free = 0.2137 target = 0.018527 restraints weight = 35705.345| |-----------------------------------------------------------------------------| r_work (final): 0.2130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 10146 Z= 0.204 Angle : 0.543 7.791 13824 Z= 0.287 Chirality : 0.047 0.138 1638 Planarity : 0.004 0.037 1770 Dihedral : 4.076 16.714 1368 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.82 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -1.16 (0.23), residues: 1290 helix: 2.07 (0.56), residues: 72 sheet: -0.61 (0.21), residues: 588 loop : -1.19 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 53 HIS 0.002 0.001 HIS G 145 PHE 0.010 0.002 PHE K 147 TYR 0.013 0.001 TYR K 170 ARG 0.004 0.000 ARG I 168 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 311) hydrogen bonds : angle 4.78361 ( 903) covalent geometry : bond 0.00450 (10146) covalent geometry : angle 0.54336 (13824) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9586 (ptp) cc_final: 0.9189 (ppp) REVERT: G 90 MET cc_start: 0.9811 (ttt) cc_final: 0.9379 (tpp) REVERT: H 56 MET cc_start: 0.9539 (ptp) cc_final: 0.9039 (ptp) REVERT: H 90 MET cc_start: 0.9574 (mtt) cc_final: 0.9374 (mtp) REVERT: I 56 MET cc_start: 0.9444 (ptp) cc_final: 0.8801 (pmm) REVERT: I 90 MET cc_start: 0.9318 (ttm) cc_final: 0.9103 (ttm) REVERT: I 177 MET cc_start: 0.8733 (tpt) cc_final: 0.8502 (mmm) REVERT: J 56 MET cc_start: 0.9594 (ptp) cc_final: 0.9298 (pmm) REVERT: J 177 MET cc_start: 0.9119 (tpt) cc_final: 0.8456 (tpt) REVERT: K 56 MET cc_start: 0.9604 (ptp) cc_final: 0.9190 (ppp) REVERT: K 90 MET cc_start: 0.9796 (ttt) cc_final: 0.9382 (tpp) REVERT: K 177 MET cc_start: 0.9248 (mmm) cc_final: 0.8966 (mmm) REVERT: L 177 MET cc_start: 0.8679 (tpt) cc_final: 0.8174 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.2817 time to fit residues: 18.8099 Evaluate side-chains 42 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.2328 r_free = 0.2328 target = 0.022283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2091 r_free = 0.2091 target = 0.017385 restraints weight = 102210.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2123 r_free = 0.2123 target = 0.018110 restraints weight = 54377.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.018620 restraints weight = 35309.912| |-----------------------------------------------------------------------------| r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10146 Z= 0.156 Angle : 0.521 8.577 13824 Z= 0.275 Chirality : 0.047 0.139 1638 Planarity : 0.004 0.031 1770 Dihedral : 3.968 16.375 1368 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: -1.15 (0.23), residues: 1290 helix: 2.24 (0.57), residues: 72 sheet: -0.62 (0.21), residues: 588 loop : -1.20 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 53 HIS 0.001 0.001 HIS K 2 PHE 0.020 0.001 PHE K 147 TYR 0.013 0.001 TYR G 170 ARG 0.004 0.000 ARG K 178 Details of bonding type rmsd hydrogen bonds : bond 0.02955 ( 311) hydrogen bonds : angle 4.71020 ( 903) covalent geometry : bond 0.00348 (10146) covalent geometry : angle 0.52071 (13824) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9569 (ptp) cc_final: 0.9249 (ppp) REVERT: G 90 MET cc_start: 0.9763 (ttt) cc_final: 0.9361 (tpp) REVERT: H 56 MET cc_start: 0.9606 (ptp) cc_final: 0.8873 (ppp) REVERT: H 177 MET cc_start: 0.9089 (tpt) cc_final: 0.8742 (tpt) REVERT: I 56 MET cc_start: 0.9423 (ptp) cc_final: 0.8810 (pmm) REVERT: I 90 MET cc_start: 0.9308 (ttm) cc_final: 0.9065 (ttm) REVERT: I 177 MET cc_start: 0.8622 (tpt) cc_final: 0.8350 (tpp) REVERT: J 56 MET cc_start: 0.9557 (ptp) cc_final: 0.9286 (pmm) REVERT: J 177 MET cc_start: 0.9147 (tpt) cc_final: 0.8660 (mmm) REVERT: K 56 MET cc_start: 0.9581 (ptp) cc_final: 0.9266 (ppp) REVERT: K 90 MET cc_start: 0.9778 (ttt) cc_final: 0.9357 (tpp) REVERT: L 169 MET cc_start: 0.9604 (ttp) cc_final: 0.9320 (ptt) REVERT: L 177 MET cc_start: 0.8519 (tpt) cc_final: 0.8057 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3045 time to fit residues: 21.4330 Evaluate side-chains 42 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.2334 r_free = 0.2334 target = 0.022381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2093 r_free = 0.2093 target = 0.017382 restraints weight = 100912.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2126 r_free = 0.2126 target = 0.018100 restraints weight = 54323.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.018611 restraints weight = 35592.181| |-----------------------------------------------------------------------------| r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10146 Z= 0.194 Angle : 0.556 10.112 13824 Z= 0.292 Chirality : 0.048 0.150 1638 Planarity : 0.004 0.030 1770 Dihedral : 4.141 16.587 1368 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.28 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.23), residues: 1290 helix: 2.34 (0.57), residues: 72 sheet: -0.69 (0.21), residues: 588 loop : -1.25 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 53 HIS 0.003 0.001 HIS G 145 PHE 0.019 0.002 PHE K 147 TYR 0.013 0.001 TYR K 170 ARG 0.004 0.001 ARG I 168 Details of bonding type rmsd hydrogen bonds : bond 0.03080 ( 311) hydrogen bonds : angle 4.80926 ( 903) covalent geometry : bond 0.00427 (10146) covalent geometry : angle 0.55644 (13824) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9561 (ptp) cc_final: 0.9227 (ppp) REVERT: G 90 MET cc_start: 0.9742 (ttt) cc_final: 0.9363 (tpp) REVERT: G 177 MET cc_start: 0.9443 (mmm) cc_final: 0.8800 (tpp) REVERT: H 56 MET cc_start: 0.9563 (ptp) cc_final: 0.9235 (ptp) REVERT: H 177 MET cc_start: 0.9111 (tpt) cc_final: 0.8693 (tpt) REVERT: I 56 MET cc_start: 0.9423 (ptp) cc_final: 0.8820 (pmm) REVERT: I 90 MET cc_start: 0.9341 (ttm) cc_final: 0.9091 (ttm) REVERT: I 177 MET cc_start: 0.8584 (tpt) cc_final: 0.8370 (tpt) REVERT: J 56 MET cc_start: 0.9534 (ptp) cc_final: 0.9270 (pmm) REVERT: J 177 MET cc_start: 0.9106 (tpt) cc_final: 0.8587 (mmm) REVERT: K 56 MET cc_start: 0.9561 (ptp) cc_final: 0.9240 (ppp) REVERT: K 90 MET cc_start: 0.9748 (ttt) cc_final: 0.9353 (tpp) REVERT: K 177 MET cc_start: 0.9367 (mmm) cc_final: 0.8751 (tpp) REVERT: L 169 MET cc_start: 0.9588 (ttp) cc_final: 0.9295 (ptt) REVERT: L 177 MET cc_start: 0.8588 (tpt) cc_final: 0.8033 (tpt) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2969 time to fit residues: 20.1160 Evaluate side-chains 40 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.2331 r_free = 0.2331 target = 0.022291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2092 r_free = 0.2092 target = 0.017344 restraints weight = 101736.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.018066 restraints weight = 54428.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2147 r_free = 0.2147 target = 0.018573 restraints weight = 35466.231| |-----------------------------------------------------------------------------| r_work (final): 0.2136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10146 Z= 0.203 Angle : 0.564 9.575 13824 Z= 0.298 Chirality : 0.048 0.146 1638 Planarity : 0.004 0.030 1770 Dihedral : 4.237 16.822 1368 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.74 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: -1.29 (0.23), residues: 1290 helix: 2.38 (0.57), residues: 72 sheet: -0.72 (0.21), residues: 588 loop : -1.32 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 53 HIS 0.002 0.001 HIS G 2 PHE 0.020 0.002 PHE G 147 TYR 0.014 0.001 TYR G 170 ARG 0.004 0.001 ARG I 168 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 311) hydrogen bonds : angle 4.84417 ( 903) covalent geometry : bond 0.00448 (10146) covalent geometry : angle 0.56443 (13824) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9553 (ptp) cc_final: 0.9141 (ppp) REVERT: G 90 MET cc_start: 0.9753 (ttt) cc_final: 0.9417 (tpp) REVERT: G 177 MET cc_start: 0.9420 (mmm) cc_final: 0.8737 (tpp) REVERT: H 56 MET cc_start: 0.9580 (ptp) cc_final: 0.8873 (ppp) REVERT: H 177 MET cc_start: 0.9174 (tpt) cc_final: 0.8820 (mmm) REVERT: I 56 MET cc_start: 0.9418 (ptp) cc_final: 0.8785 (pmm) REVERT: I 90 MET cc_start: 0.9355 (ttm) cc_final: 0.9107 (ttm) REVERT: J 56 MET cc_start: 0.9511 (ptp) cc_final: 0.9172 (pmm) REVERT: J 177 MET cc_start: 0.9185 (tpt) cc_final: 0.8687 (mmm) REVERT: K 56 MET cc_start: 0.9559 (ptp) cc_final: 0.9184 (ppp) REVERT: K 90 MET cc_start: 0.9740 (ttt) cc_final: 0.9398 (tpp) REVERT: L 169 MET cc_start: 0.9580 (ttp) cc_final: 0.9287 (ptt) REVERT: L 177 MET cc_start: 0.8571 (tpt) cc_final: 0.8067 (tpt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.2601 time to fit residues: 16.8833 Evaluate side-chains 41 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.2333 r_free = 0.2333 target = 0.022272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2093 r_free = 0.2093 target = 0.017341 restraints weight = 101572.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2126 r_free = 0.2126 target = 0.018063 restraints weight = 54455.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2149 r_free = 0.2149 target = 0.018570 restraints weight = 35463.496| |-----------------------------------------------------------------------------| r_work (final): 0.2139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10146 Z= 0.189 Angle : 0.575 15.446 13824 Z= 0.299 Chirality : 0.048 0.143 1638 Planarity : 0.004 0.030 1770 Dihedral : 4.248 16.592 1368 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: -1.33 (0.23), residues: 1290 helix: 2.40 (0.57), residues: 72 sheet: -0.74 (0.21), residues: 588 loop : -1.34 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 53 HIS 0.002 0.001 HIS G 145 PHE 0.021 0.002 PHE G 147 TYR 0.014 0.001 TYR G 170 ARG 0.009 0.000 ARG I 168 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 311) hydrogen bonds : angle 4.81541 ( 903) covalent geometry : bond 0.00421 (10146) covalent geometry : angle 0.57519 (13824) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2580 Ramachandran restraints generated. 1290 Oldfield, 0 Emsley, 1290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.086 Fit side-chains REVERT: G 56 MET cc_start: 0.9540 (ptp) cc_final: 0.9138 (ppp) REVERT: G 90 MET cc_start: 0.9729 (ttt) cc_final: 0.9398 (tpp) REVERT: G 177 MET cc_start: 0.9384 (mmm) cc_final: 0.8687 (tpp) REVERT: H 56 MET cc_start: 0.9576 (ptp) cc_final: 0.8914 (ppp) REVERT: H 173 LYS cc_start: 0.9612 (mmtt) cc_final: 0.9409 (tptp) REVERT: H 177 MET cc_start: 0.9170 (tpt) cc_final: 0.8667 (mmm) REVERT: I 56 MET cc_start: 0.9405 (ptp) cc_final: 0.8793 (pmm) REVERT: I 90 MET cc_start: 0.9360 (ttm) cc_final: 0.9127 (ttm) REVERT: I 177 MET cc_start: 0.8671 (tpt) cc_final: 0.8033 (tpp) REVERT: J 56 MET cc_start: 0.9540 (ptp) cc_final: 0.9215 (pmm) REVERT: J 173 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9416 (tptp) REVERT: J 177 MET cc_start: 0.9180 (tpt) cc_final: 0.8643 (mmm) REVERT: K 56 MET cc_start: 0.9554 (ptp) cc_final: 0.9171 (ppp) REVERT: K 90 MET cc_start: 0.9738 (ttt) cc_final: 0.9404 (tpp) REVERT: L 169 MET cc_start: 0.9571 (ttp) cc_final: 0.9291 (ptt) REVERT: L 177 MET cc_start: 0.8569 (tpt) cc_final: 0.8063 (tpt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2464 time to fit residues: 15.6905 Evaluate side-chains 42 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 9.9990 chunk 18 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 0.3980 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 163 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2346 r_free = 0.2346 target = 0.022550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2104 r_free = 0.2104 target = 0.017527 restraints weight = 101197.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.018260 restraints weight = 54474.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2161 r_free = 0.2161 target = 0.018776 restraints weight = 35677.624| |-----------------------------------------------------------------------------| r_work (final): 0.2151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9084 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10146 Z= 0.135 Angle : 0.538 13.240 13824 Z= 0.280 Chirality : 0.048 0.149 1638 Planarity : 0.004 0.032 1770 Dihedral : 4.041 16.626 1368 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.89 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: -1.26 (0.23), residues: 1290 helix: 2.44 (0.58), residues: 72 sheet: -0.65 (0.21), residues: 582 loop : -1.35 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 53 HIS 0.001 0.000 HIS G 145 PHE 0.015 0.001 PHE G 147 TYR 0.014 0.001 TYR G 170 ARG 0.007 0.000 ARG I 168 Details of bonding type rmsd hydrogen bonds : bond 0.02888 ( 311) hydrogen bonds : angle 4.67811 ( 903) covalent geometry : bond 0.00307 (10146) covalent geometry : angle 0.53789 (13824) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.58 seconds wall clock time: 41 minutes 27.30 seconds (2487.30 seconds total)