Starting phenix.real_space_refine on Wed Sep 17 17:01:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l0f_62699/09_2025/9l0f_62699.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l0f_62699/09_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_62699/09_2025/9l0f_62699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l0f_62699/09_2025/9l0f_62699.map" model { file = "/net/cci-nas-00/data/ceres_data/9l0f_62699/09_2025/9l0f_62699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l0f_62699/09_2025/9l0f_62699.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.33, per 1000 atoms: 0.23 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: 0.92 Conformation dependent library (CDL) restraints added in 317.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.42 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: 1.43 Time building geometry restraints manager: 1.15 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: 0.01 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: 0.970 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.740 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (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 ARG 0.004 0.001 ARG H 178 TYR 0.013 0.001 TYR G 170 PHE 0.028 0.002 PHE J 147 TRP 0.007 0.001 TRP G 180 HIS 0.001 0.000 HIS L 145 Details of bonding type rmsd covalent geometry : bond 0.00354 (10146) covalent geometry : angle 0.61454 (13824) hydrogen bonds : bond 0.23485 ( 311) hydrogen bonds : angle 7.93948 ( 903) *********************** 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 : 0.388 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 69 average time/residue: 0.1287 time to fit residues: 11.8473 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 : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 6.0990 ------------------------------------------------------------------------------- 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 = 0.2396 r_free = 0.2396 target = 0.024554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2157 r_free = 0.2157 target = 0.019250 restraints weight = 96157.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.020016 restraints weight = 52351.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.020558 restraints weight = 34475.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2224 r_free = 0.2224 target = 0.020932 restraints weight = 25257.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.021217 restraints weight = 20002.389| |-----------------------------------------------------------------------------| r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10146 Z= 0.190 Angle : 0.571 5.039 13824 Z= 0.307 Chirality : 0.048 0.162 1638 Planarity : 0.004 0.036 1770 Dihedral : 4.094 16.371 1368 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.28 % Favored : 93.49 % Rotamer: Outliers : 0.09 % Allowed : 4.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.23), residues: 1290 helix: 1.68 (0.59), residues: 72 sheet: -0.13 (0.23), residues: 546 loop : -1.37 (0.21), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 178 TYR 0.012 0.001 TYR K 170 PHE 0.019 0.002 PHE J 84 TRP 0.009 0.001 TRP H 53 HIS 0.002 0.001 HIS I 145 Details of bonding type rmsd covalent geometry : bond 0.00428 (10146) covalent geometry : angle 0.57104 (13824) hydrogen bonds : bond 0.03686 ( 311) hydrogen bonds : angle 5.52946 ( 903) *********************** 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 55 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 90 MET cc_start: 0.9712 (ttt) cc_final: 0.9068 (tmm) REVERT: G 207 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9297 (mmmm) REVERT: H 56 MET cc_start: 0.8800 (ppp) cc_final: 0.8112 (ppp) REVERT: H 177 MET cc_start: 0.8539 (tpp) cc_final: 0.8202 (tpt) REVERT: I 56 MET cc_start: 0.9415 (ptp) cc_final: 0.8750 (pmm) REVERT: J 56 MET cc_start: 0.9612 (ptp) cc_final: 0.9266 (pmm) REVERT: J 90 MET cc_start: 0.9472 (ttm) cc_final: 0.8884 (tmm) REVERT: J 177 MET cc_start: 0.8497 (tpp) cc_final: 0.8195 (tpt) REVERT: J 207 LYS cc_start: 0.8810 (mmtm) cc_final: 0.8510 (mmtt) REVERT: K 90 MET cc_start: 0.9713 (ttt) cc_final: 0.9027 (tmm) REVERT: L 56 MET cc_start: 0.9407 (ptp) cc_final: 0.8845 (pmm) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1388 time to fit residues: 10.1097 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 91 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 overall best weight: 7.4126 ------------------------------------------------------------------------------- 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 K 114 GLN K 145 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.022679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2093 r_free = 0.2093 target = 0.017707 restraints weight = 101349.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.018416 restraints weight = 54147.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2146 r_free = 0.2146 target = 0.018921 restraints weight = 35495.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2161 r_free = 0.2161 target = 0.019282 restraints weight = 25855.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.019541 restraints weight = 20287.230| |-----------------------------------------------------------------------------| r_work (final): 0.2169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10146 Z= 0.215 Angle : 0.560 6.130 13824 Z= 0.301 Chirality : 0.048 0.140 1638 Planarity : 0.004 0.039 1770 Dihedral : 4.268 16.387 1368 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.89 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.23), residues: 1290 helix: 1.73 (0.58), residues: 72 sheet: -0.68 (0.21), residues: 624 loop : -1.45 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 178 TYR 0.007 0.001 TYR K 170 PHE 0.014 0.002 PHE J 84 TRP 0.010 0.001 TRP H 53 HIS 0.002 0.001 HIS I 145 Details of bonding type rmsd covalent geometry : bond 0.00478 (10146) covalent geometry : angle 0.55961 (13824) hydrogen bonds : bond 0.03495 ( 311) hydrogen bonds : angle 5.20546 ( 903) *********************** 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 : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9019 (ppp) cc_final: 0.8716 (ppp) REVERT: G 90 MET cc_start: 0.9699 (ttt) cc_final: 0.9379 (tpp) REVERT: G 207 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9310 (mmmm) REVERT: H 56 MET cc_start: 0.9041 (ppp) cc_final: 0.8012 (ppp) REVERT: I 169 MET cc_start: 0.9638 (ttm) cc_final: 0.9256 (ttm) REVERT: I 177 MET cc_start: 0.8778 (tpt) cc_final: 0.8250 (tpt) REVERT: J 56 MET cc_start: 0.9630 (ptp) cc_final: 0.8866 (pmm) REVERT: J 90 MET cc_start: 0.9503 (ttm) cc_final: 0.8828 (tmm) REVERT: J 177 MET cc_start: 0.8538 (tpp) cc_final: 0.8095 (tpt) REVERT: J 207 LYS cc_start: 0.8946 (mmtm) cc_final: 0.8679 (mptt) REVERT: K 56 MET cc_start: 0.9014 (ppp) cc_final: 0.8688 (ppp) REVERT: K 90 MET cc_start: 0.9697 (ttt) cc_final: 0.9369 (tpp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1536 time to fit residues: 10.7979 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 2 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 2 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2320 r_free = 0.2320 target = 0.022246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2082 r_free = 0.2082 target = 0.017294 restraints weight = 102647.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2113 r_free = 0.2113 target = 0.018004 restraints weight = 55246.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.018504 restraints weight = 36243.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.018861 restraints weight = 26456.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2163 r_free = 0.2163 target = 0.019115 restraints weight = 20812.567| |-----------------------------------------------------------------------------| r_work (final): 0.2153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9092 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 10146 Z= 0.251 Angle : 0.579 6.230 13824 Z= 0.311 Chirality : 0.048 0.144 1638 Planarity : 0.004 0.035 1770 Dihedral : 4.471 16.741 1368 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.67 % Favored : 93.02 % Rotamer: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.23), residues: 1290 helix: 1.80 (0.56), residues: 72 sheet: -0.77 (0.20), residues: 612 loop : -1.29 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 178 TYR 0.010 0.001 TYR G 170 PHE 0.012 0.002 PHE K 147 TRP 0.014 0.002 TRP G 53 HIS 0.002 0.001 HIS G 145 Details of bonding type rmsd covalent geometry : bond 0.00550 (10146) covalent geometry : angle 0.57901 (13824) hydrogen bonds : bond 0.03430 ( 311) hydrogen bonds : angle 5.10404 ( 903) *********************** 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 48 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9169 (ppp) cc_final: 0.8853 (ppp) REVERT: G 90 MET cc_start: 0.9719 (ttt) cc_final: 0.9487 (tpp) REVERT: G 177 MET cc_start: 0.9232 (mmm) cc_final: 0.8909 (mmm) REVERT: H 56 MET cc_start: 0.9435 (ppp) cc_final: 0.9167 (ppp) REVERT: I 169 MET cc_start: 0.9699 (ttm) cc_final: 0.9380 (ttm) REVERT: I 177 MET cc_start: 0.8941 (tpt) cc_final: 0.8516 (tpt) REVERT: J 56 MET cc_start: 0.9543 (ptp) cc_final: 0.9201 (pmm) REVERT: J 207 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8665 (mptt) REVERT: K 56 MET cc_start: 0.9166 (ppp) cc_final: 0.8845 (ppp) REVERT: K 90 MET cc_start: 0.9722 (ttt) cc_final: 0.9476 (tpp) REVERT: L 177 MET cc_start: 0.8696 (tpt) cc_final: 0.8466 (tpt) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1192 time to fit residues: 7.8538 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 : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.2334 r_free = 0.2334 target = 0.022402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2092 r_free = 0.2092 target = 0.017418 restraints weight = 101744.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2125 r_free = 0.2125 target = 0.018134 restraints weight = 54847.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.018645 restraints weight = 35800.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2165 r_free = 0.2165 target = 0.019004 restraints weight = 26132.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2177 r_free = 0.2177 target = 0.019259 restraints weight = 20530.893| |-----------------------------------------------------------------------------| r_work (final): 0.2167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.3526 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= 0.173 Angle : 0.527 4.970 13824 Z= 0.283 Chirality : 0.048 0.141 1638 Planarity : 0.004 0.032 1770 Dihedral : 4.239 18.312 1368 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.12 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.23), residues: 1290 helix: 2.17 (0.57), residues: 72 sheet: -0.65 (0.21), residues: 588 loop : -1.19 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 178 TYR 0.012 0.001 TYR G 170 PHE 0.011 0.001 PHE L 84 TRP 0.011 0.001 TRP K 53 HIS 0.001 0.000 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00382 (10146) covalent geometry : angle 0.52664 (13824) hydrogen bonds : bond 0.03146 ( 311) hydrogen bonds : angle 4.83778 ( 903) *********************** 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 : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9203 (ppp) cc_final: 0.8814 (ppp) REVERT: G 90 MET cc_start: 0.9713 (ttt) cc_final: 0.9489 (tpp) REVERT: I 56 MET cc_start: 0.9419 (ptp) cc_final: 0.9183 (ptp) REVERT: I 90 MET cc_start: 0.9267 (ttm) cc_final: 0.9030 (ttm) REVERT: I 177 MET cc_start: 0.8552 (tpt) cc_final: 0.8320 (mmm) REVERT: J 56 MET cc_start: 0.9560 (ptp) cc_final: 0.9229 (pmm) REVERT: J 177 MET cc_start: 0.8925 (tpp) cc_final: 0.8721 (tpt) REVERT: J 207 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8697 (mptt) REVERT: K 56 MET cc_start: 0.9191 (ppp) cc_final: 0.8798 (ppp) REVERT: K 90 MET cc_start: 0.9729 (ttt) cc_final: 0.9489 (tpp) REVERT: L 56 MET cc_start: 0.9417 (ptp) cc_final: 0.9170 (ptp) REVERT: L 177 MET cc_start: 0.8720 (tpt) cc_final: 0.8155 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1350 time to fit residues: 9.5125 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 5.9990 chunk 35 optimal weight: 0.0870 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 163 GLN H 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 = 0.2354 r_free = 0.2354 target = 0.022835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.017880 restraints weight = 100931.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2151 r_free = 0.2151 target = 0.018615 restraints weight = 53297.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.019128 restraints weight = 34383.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2189 r_free = 0.2189 target = 0.019490 restraints weight = 24890.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2200 r_free = 0.2200 target = 0.019743 restraints weight = 19459.441| |-----------------------------------------------------------------------------| r_work (final): 0.2194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10146 Z= 0.100 Angle : 0.505 7.355 13824 Z= 0.266 Chirality : 0.048 0.156 1638 Planarity : 0.004 0.032 1770 Dihedral : 3.890 15.758 1368 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.97 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.23), residues: 1290 helix: 2.33 (0.58), residues: 72 sheet: -0.47 (0.21), residues: 582 loop : -1.20 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 168 TYR 0.014 0.001 TYR G 170 PHE 0.017 0.001 PHE K 147 TRP 0.009 0.001 TRP K 53 HIS 0.001 0.000 HIS K 145 Details of bonding type rmsd covalent geometry : bond 0.00223 (10146) covalent geometry : angle 0.50510 (13824) hydrogen bonds : bond 0.02812 ( 311) hydrogen bonds : angle 4.58368 ( 903) *********************** 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 47 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9256 (ppp) cc_final: 0.8928 (ppp) REVERT: G 90 MET cc_start: 0.9665 (ttt) cc_final: 0.9375 (tpp) REVERT: H 177 MET cc_start: 0.9180 (tpt) cc_final: 0.8728 (tpt) REVERT: I 56 MET cc_start: 0.9389 (ptp) cc_final: 0.9155 (ptp) REVERT: I 177 MET cc_start: 0.8370 (tpt) cc_final: 0.8048 (tpt) REVERT: J 56 MET cc_start: 0.9555 (ptp) cc_final: 0.9205 (pmm) REVERT: J 207 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8675 (mptt) REVERT: K 56 MET cc_start: 0.9245 (ppp) cc_final: 0.8930 (ppp) REVERT: K 90 MET cc_start: 0.9685 (ttt) cc_final: 0.9420 (tpp) REVERT: L 56 MET cc_start: 0.9373 (ptp) cc_final: 0.9122 (ptp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1273 time to fit residues: 8.3864 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 : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 83 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 21 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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 = 0.2348 r_free = 0.2348 target = 0.022717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2109 r_free = 0.2109 target = 0.017676 restraints weight = 101105.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2141 r_free = 0.2141 target = 0.018395 restraints weight = 54264.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2165 r_free = 0.2165 target = 0.018918 restraints weight = 35682.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2181 r_free = 0.2181 target = 0.019283 restraints weight = 25967.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2193 r_free = 0.2193 target = 0.019545 restraints weight = 20453.000| |-----------------------------------------------------------------------------| r_work (final): 0.2186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10146 Z= 0.140 Angle : 0.518 6.792 13824 Z= 0.273 Chirality : 0.048 0.145 1638 Planarity : 0.004 0.032 1770 Dihedral : 3.885 15.954 1368 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.23), residues: 1290 helix: 2.42 (0.58), residues: 72 sheet: -0.51 (0.21), residues: 582 loop : -1.20 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 178 TYR 0.012 0.001 TYR G 170 PHE 0.015 0.001 PHE K 147 TRP 0.009 0.001 TRP G 53 HIS 0.001 0.000 HIS K 2 Details of bonding type rmsd covalent geometry : bond 0.00314 (10146) covalent geometry : angle 0.51828 (13824) hydrogen bonds : bond 0.03050 ( 311) hydrogen bonds : angle 4.57923 ( 903) *********************** 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 47 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9260 (ppp) cc_final: 0.8921 (ppp) REVERT: G 90 MET cc_start: 0.9701 (ttt) cc_final: 0.9367 (tpt) REVERT: G 177 MET cc_start: 0.9318 (mmm) cc_final: 0.9084 (tpp) REVERT: H 169 MET cc_start: 0.9482 (ttp) cc_final: 0.9077 (ttp) REVERT: H 177 MET cc_start: 0.9149 (tpt) cc_final: 0.8798 (mmm) REVERT: I 56 MET cc_start: 0.9404 (ptp) cc_final: 0.9184 (ptp) REVERT: I 90 MET cc_start: 0.9288 (ttm) cc_final: 0.9085 (ttm) REVERT: J 56 MET cc_start: 0.9530 (ptp) cc_final: 0.9182 (pmm) REVERT: J 177 MET cc_start: 0.9077 (mmm) cc_final: 0.8856 (tpt) REVERT: K 56 MET cc_start: 0.9245 (ppp) cc_final: 0.8906 (ppp) REVERT: K 90 MET cc_start: 0.9700 (ttt) cc_final: 0.9352 (tpt) REVERT: K 207 LYS cc_start: 0.9371 (mmmm) cc_final: 0.8705 (mmtm) REVERT: L 56 MET cc_start: 0.9403 (ptp) cc_final: 0.9161 (ptp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1286 time to fit residues: 8.3333 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 : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 145 HIS I 114 GLN L 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2311 r_free = 0.2311 target = 0.021939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2072 r_free = 0.2072 target = 0.017008 restraints weight = 104196.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2103 r_free = 0.2103 target = 0.017697 restraints weight = 56639.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2125 r_free = 0.2125 target = 0.018181 restraints weight = 37401.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2140 r_free = 0.2140 target = 0.018521 restraints weight = 27537.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2152 r_free = 0.2152 target = 0.018772 restraints weight = 21870.940| |-----------------------------------------------------------------------------| r_work (final): 0.2147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10146 Z= 0.249 Angle : 0.589 5.844 13824 Z= 0.313 Chirality : 0.048 0.145 1638 Planarity : 0.004 0.029 1770 Dihedral : 4.299 18.613 1368 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.24), residues: 1290 helix: 2.52 (0.58), residues: 72 sheet: -0.68 (0.21), residues: 582 loop : -1.03 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 178 TYR 0.014 0.001 TYR K 170 PHE 0.018 0.002 PHE K 147 TRP 0.014 0.002 TRP J 53 HIS 0.002 0.001 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00547 (10146) covalent geometry : angle 0.58908 (13824) hydrogen bonds : bond 0.03390 ( 311) hydrogen bonds : angle 4.81049 ( 903) *********************** 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 45 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 56 MET cc_start: 0.9246 (ppp) cc_final: 0.8828 (ppp) REVERT: G 90 MET cc_start: 0.9711 (ttt) cc_final: 0.9343 (tpt) REVERT: H 169 MET cc_start: 0.9327 (ttp) cc_final: 0.8759 (ptm) REVERT: H 177 MET cc_start: 0.9259 (tpt) cc_final: 0.8808 (mmm) REVERT: I 56 MET cc_start: 0.9429 (ptp) cc_final: 0.9164 (ptp) REVERT: I 177 MET cc_start: 0.8280 (tpt) cc_final: 0.7977 (tpt) REVERT: J 56 MET cc_start: 0.9452 (ptp) cc_final: 0.9127 (pmm) REVERT: J 207 LYS cc_start: 0.9630 (mmmm) cc_final: 0.8900 (mmtt) REVERT: K 56 MET cc_start: 0.9227 (ppp) cc_final: 0.8856 (ppp) REVERT: K 90 MET cc_start: 0.9717 (ttt) cc_final: 0.9477 (tpp) REVERT: L 56 MET cc_start: 0.9484 (ptp) cc_final: 0.9258 (ptp) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1170 time to fit residues: 7.5461 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 : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.022322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2091 r_free = 0.2091 target = 0.017301 restraints weight = 102003.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2124 r_free = 0.2124 target = 0.018009 restraints weight = 54749.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2147 r_free = 0.2147 target = 0.018521 restraints weight = 36057.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2164 r_free = 0.2164 target = 0.018879 restraints weight = 26269.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2175 r_free = 0.2175 target = 0.019131 restraints weight = 20669.151| |-----------------------------------------------------------------------------| r_work (final): 0.2170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9070 moved from start: 0.3824 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= 0.149 Angle : 0.552 12.574 13824 Z= 0.288 Chirality : 0.048 0.156 1638 Planarity : 0.004 0.032 1770 Dihedral : 4.134 16.502 1368 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.89 % Favored : 94.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.24), residues: 1290 helix: 2.46 (0.58), residues: 72 sheet: -0.65 (0.21), residues: 582 loop : -1.03 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 168 TYR 0.011 0.001 TYR G 170 PHE 0.013 0.001 PHE K 147 TRP 0.011 0.001 TRP I 53 HIS 0.001 0.000 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00335 (10146) covalent geometry : angle 0.55244 (13824) hydrogen bonds : bond 0.03128 ( 311) hydrogen bonds : angle 4.73058 ( 903) *********************** 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 50 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: G 56 MET cc_start: 0.9291 (ppp) cc_final: 0.8917 (ppp) REVERT: G 90 MET cc_start: 0.9714 (ttt) cc_final: 0.9326 (tpt) REVERT: G 177 MET cc_start: 0.9198 (mmm) cc_final: 0.8972 (tpt) REVERT: H 169 MET cc_start: 0.9288 (ttp) cc_final: 0.8817 (ptm) REVERT: H 173 LYS cc_start: 0.9674 (mmtt) cc_final: 0.9411 (tptp) REVERT: H 177 MET cc_start: 0.9174 (tpt) cc_final: 0.8706 (mmm) REVERT: I 177 MET cc_start: 0.8156 (tpt) cc_final: 0.7890 (tpp) REVERT: J 56 MET cc_start: 0.9504 (ptp) cc_final: 0.9148 (pmm) REVERT: J 177 MET cc_start: 0.9097 (tpt) cc_final: 0.8813 (tpt) REVERT: J 207 LYS cc_start: 0.9621 (mmmm) cc_final: 0.8812 (mmtt) REVERT: K 56 MET cc_start: 0.9266 (ppp) cc_final: 0.8840 (ppp) REVERT: K 90 MET cc_start: 0.9729 (ttt) cc_final: 0.9333 (tpt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1328 time to fit residues: 8.9994 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 88 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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 = 0.2329 r_free = 0.2329 target = 0.022214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2088 r_free = 0.2088 target = 0.017281 restraints weight = 102210.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2120 r_free = 0.2120 target = 0.017980 restraints weight = 55739.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.018476 restraints weight = 36709.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2160 r_free = 0.2160 target = 0.018824 restraints weight = 26964.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2171 r_free = 0.2171 target = 0.019073 restraints weight = 21329.335| |-----------------------------------------------------------------------------| r_work (final): 0.2165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10146 Z= 0.172 Angle : 0.559 10.812 13824 Z= 0.291 Chirality : 0.048 0.145 1638 Planarity : 0.004 0.031 1770 Dihedral : 4.143 16.691 1368 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.23), residues: 1290 helix: 2.47 (0.58), residues: 72 sheet: -0.78 (0.21), residues: 600 loop : -1.20 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 168 TYR 0.012 0.001 TYR G 170 PHE 0.015 0.001 PHE K 147 TRP 0.011 0.001 TRP J 53 HIS 0.002 0.000 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00383 (10146) covalent geometry : angle 0.55930 (13824) hydrogen bonds : bond 0.03160 ( 311) hydrogen bonds : angle 4.75420 ( 903) ********************** 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 47 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: G 56 MET cc_start: 0.9290 (ppp) cc_final: 0.8872 (ppp) REVERT: G 90 MET cc_start: 0.9694 (ttt) cc_final: 0.9326 (tpt) REVERT: H 169 MET cc_start: 0.9305 (ttp) cc_final: 0.8812 (ptm) REVERT: H 173 LYS cc_start: 0.9659 (mmtt) cc_final: 0.9420 (tptp) REVERT: H 177 MET cc_start: 0.9263 (tpt) cc_final: 0.8797 (mmm) REVERT: I 177 MET cc_start: 0.8285 (tpt) cc_final: 0.7996 (tpp) REVERT: J 56 MET cc_start: 0.9513 (ptp) cc_final: 0.9179 (pmm) REVERT: J 177 MET cc_start: 0.9190 (tpt) cc_final: 0.8419 (tpt) REVERT: K 56 MET cc_start: 0.9277 (ppp) cc_final: 0.8857 (ppp) REVERT: K 90 MET cc_start: 0.9719 (ttt) cc_final: 0.9338 (tpt) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1418 time to fit residues: 9.2308 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 : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 68 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.2332 r_free = 0.2332 target = 0.022247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2094 r_free = 0.2094 target = 0.017335 restraints weight = 103190.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2126 r_free = 0.2126 target = 0.018018 restraints weight = 56024.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2148 r_free = 0.2148 target = 0.018512 restraints weight = 37178.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2165 r_free = 0.2165 target = 0.018864 restraints weight = 27271.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2176 r_free = 0.2176 target = 0.019112 restraints weight = 21505.847| |-----------------------------------------------------------------------------| r_work (final): 0.2167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10146 Z= 0.172 Angle : 0.556 9.429 13824 Z= 0.293 Chirality : 0.048 0.151 1638 Planarity : 0.004 0.031 1770 Dihedral : 4.241 18.981 1368 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.89 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.24), residues: 1290 helix: 2.48 (0.58), residues: 72 sheet: -0.76 (0.21), residues: 594 loop : -1.03 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 178 TYR 0.012 0.001 TYR G 170 PHE 0.013 0.001 PHE K 147 TRP 0.012 0.001 TRP H 53 HIS 0.002 0.000 HIS G 2 Details of bonding type rmsd covalent geometry : bond 0.00383 (10146) covalent geometry : angle 0.55640 (13824) hydrogen bonds : bond 0.03162 ( 311) hydrogen bonds : angle 4.73961 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1222.97 seconds wall clock time: 22 minutes 8.89 seconds (1328.89 seconds total)