Starting phenix.real_space_refine on Mon Nov 17 18:06:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.map" model { file = "/net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f36_4176/11_2025/6f36_4176.cif" } resolution = 3.7 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= 0.001 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 40 5.16 5 C 4930 2.51 5 N 1204 2.21 5 O 1279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7453 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 509 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 1, 'TRANS': 71} Chain: "M" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1730 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 15, 'TRANS': 212} Chain: "N" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 633 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 1.46, per 1000 atoms: 0.20 Number of scatterers: 7453 At special positions: 0 Unit cell: (104.975, 98.345, 130.39, 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 40 16.00 O 1279 8.00 N 1204 7.00 C 4930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" CA THR D 110 " - pdb=" N GLU D 111 " distance=2.45 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: 0.63 Conformation dependent library (CDL) restraints added in 448.1 milliseconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 85.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 126 removed outlier: 4.110A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.689A pdb=" N GLY C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.294A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.804A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 85 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 126 removed outlier: 4.108A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY F 65 " --> pdb=" O MET F 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 85 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.806A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY G 65 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 85 " --> pdb=" O MET G 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.805A pdb=" N LYS H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 85 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 126 removed outlier: 4.108A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU I 85 " --> pdb=" O MET I 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.804A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY J 65 " --> pdb=" O MET J 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE J 116 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 134 through 142 removed outlier: 3.856A pdb=" N ASP M 140 " --> pdb=" O PRO M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.613A pdb=" N TRP M 151 " --> pdb=" O SER M 147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE M 155 " --> pdb=" O TRP M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 185 through 190 removed outlier: 3.609A pdb=" N TRP M 189 " --> pdb=" O GLY M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 195 removed outlier: 3.540A pdb=" N LEU M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 226 removed outlier: 4.007A pdb=" N PHE M 221 " --> pdb=" O MET M 217 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL M 222 " --> pdb=" O ALA M 218 " (cutoff:3.500A) Proline residue: M 223 - end of helix Processing helix chain 'M' and resid 226 through 259 removed outlier: 4.352A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER M 235 " --> pdb=" O PHE M 231 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG M 239 " --> pdb=" O SER M 235 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET M 244 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU M 251 " --> pdb=" O GLY M 247 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS M 252 " --> pdb=" O HIS M 248 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE M 253 " --> pdb=" O THR M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 265 Processing helix chain 'M' and resid 273 through 309 removed outlier: 3.679A pdb=" N LEU M 284 " --> pdb=" O LEU M 280 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU M 287 " --> pdb=" O ALA M 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 294 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY M 297 " --> pdb=" O VAL M 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE M 301 " --> pdb=" O GLY M 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 78 Processing helix chain 'N' and resid 83 through 91 removed outlier: 3.515A pdb=" N ASP N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 110 removed outlier: 3.535A pdb=" N ASP N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN N 106 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 118 removed outlier: 3.635A pdb=" N SER N 117 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER N 118 " --> pdb=" O ILE N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 130 removed outlier: 4.557A pdb=" N PHE N 127 " --> pdb=" O ARG N 123 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1392 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: 1.10 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1 1.11 - 1.29: 1143 1.29 - 1.46: 3001 1.46 - 1.64: 3371 1.64 - 1.81: 66 Bond restraints: 7582 Sorted by residual: bond pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 1.334 0.940 0.394 1.43e-02 4.89e+03 7.59e+02 bond pdb=" CB TRP M 151 " pdb=" CG TRP M 151 " ideal model delta sigma weight residual 1.498 1.417 0.081 3.10e-02 1.04e+03 6.89e+00 bond pdb=" CB ARG N 89 " pdb=" CG ARG N 89 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.05e+00 bond pdb=" CG LEU M 245 " pdb=" CD2 LEU M 245 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.73e+00 bond pdb=" C ARG M 239 " pdb=" N LEU M 240 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.38e-02 5.25e+03 5.48e+00 ... (remaining 7577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9662 2.09 - 4.18: 491 4.18 - 6.28: 108 6.28 - 8.37: 22 8.37 - 10.46: 6 Bond angle restraints: 10289 Sorted by residual: angle pdb=" N ARG M 239 " pdb=" CA ARG M 239 " pdb=" C ARG M 239 " ideal model delta sigma weight residual 111.69 105.29 6.40 1.23e+00 6.61e-01 2.70e+01 angle pdb=" CA VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 118.40 112.73 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" N GLY M 317 " pdb=" CA GLY M 317 " pdb=" C GLY M 317 " ideal model delta sigma weight residual 112.34 121.03 -8.69 2.04e+00 2.40e-01 1.81e+01 angle pdb=" C PRO M 169 " pdb=" N PHE M 170 " pdb=" CA PHE M 170 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 angle pdb=" O VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 122.17 126.78 -4.61 1.23e+00 6.61e-01 1.41e+01 ... (remaining 10284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 4013 14.81 - 29.61: 261 29.61 - 44.42: 74 44.42 - 59.22: 3 59.22 - 74.03: 2 Dihedral angle restraints: 4353 sinusoidal: 1483 harmonic: 2870 Sorted by residual: dihedral pdb=" CA PRO M 223 " pdb=" C PRO M 223 " pdb=" N LEU M 224 " pdb=" CA LEU M 224 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE N 80 " pdb=" C PHE N 80 " pdb=" N GLY N 81 " pdb=" CA GLY N 81 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER M 187 " pdb=" C SER M 187 " pdb=" N VAL M 188 " pdb=" CA VAL M 188 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 968 0.068 - 0.137: 289 0.137 - 0.205: 17 0.205 - 0.273: 0 0.273 - 0.341: 12 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1283 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO M 262 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 222 " 0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO M 223 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO M 223 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 204 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO M 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 205 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 205 " -0.037 5.00e-02 4.00e+02 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2504 2.82 - 3.34: 7173 3.34 - 3.86: 11838 3.86 - 4.38: 15001 4.38 - 4.90: 23179 Nonbonded interactions: 59695 Sorted by model distance: nonbonded pdb=" O VAL M 238 " pdb=" CA ARG M 239 " model vdw 2.304 2.776 nonbonded pdb=" O ALA H 58 " pdb=" OG SER I 59 " model vdw 2.349 3.040 nonbonded pdb=" OD2 ASP M 140 " pdb=" NZ LYS M 144 " model vdw 2.379 3.120 nonbonded pdb=" O ASN M 121 " pdb=" NH2 ARG M 145 " model vdw 2.405 3.120 nonbonded pdb=" O SER M 142 " pdb=" OG SER M 142 " model vdw 2.439 3.040 ... (remaining 59690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 9.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.070 Find NCS groups from input model: 0.100 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 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 : 0.011 0.417 7583 Z= 0.543 Angle : 1.313 66.873 10291 Z= 0.649 Chirality : 0.065 0.341 1286 Planarity : 0.007 0.077 1259 Dihedral : 11.061 74.029 2524 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.27 % Allowed : 9.57 % Favored : 90.16 % 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 are not related in a simple way. whole: -5.92 (0.20), residues: 1015 helix: -4.08 (0.10), residues: 793 sheet: None (None), residues: 0 loop : -1.96 (0.48), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 130 TYR 0.016 0.003 TYR M 114 PHE 0.029 0.003 PHE M 204 TRP 0.031 0.004 TRP M 189 HIS 0.020 0.003 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00984 ( 7582) covalent geometry : angle 1.13476 (10289) SS BOND : bond 0.41709 ( 1) SS BOND : angle 47.38480 ( 2) hydrogen bonds : bond 0.29303 ( 465) hydrogen bonds : angle 10.28637 ( 1392) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 220 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.7963 (m) cc_final: 0.7712 (p) REVERT: D 113 ILE cc_start: 0.6589 (mm) cc_final: 0.6287 (mm) REVERT: E 69 ILE cc_start: 0.7754 (mt) cc_final: 0.7530 (mm) REVERT: E 87 ASN cc_start: 0.5815 (t0) cc_final: 0.5352 (t0) REVERT: H 95 ILE cc_start: 0.5632 (tt) cc_final: 0.5123 (mt) REVERT: H 115 LEU cc_start: 0.5771 (mm) cc_final: 0.5513 (tt) REVERT: M 132 ASP cc_start: 0.7950 (m-30) cc_final: 0.7591 (m-30) REVERT: M 229 TYR cc_start: 0.7730 (t80) cc_final: 0.7484 (t80) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.0718 time to fit residues: 22.7455 Evaluate side-chains 117 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.0870 chunk 97 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN M 243 ASN M 252 HIS N 93 GLN N 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.138817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 132)---------------| | r_work = 0.4042 r_free = 0.4042 target = 0.124785 restraints weight = 20265.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.124656 restraints weight = 22023.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.124499 restraints weight = 13650.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.124137 restraints weight = 12229.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.124149 restraints weight = 13303.567| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.210 7583 Z= 0.205 Angle : 0.759 27.508 10291 Z= 0.377 Chirality : 0.042 0.276 1286 Planarity : 0.005 0.048 1259 Dihedral : 6.088 45.967 1064 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 4.39 % Allowed : 17.02 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -4.07 (0.22), residues: 1015 helix: -2.61 (0.14), residues: 811 sheet: None (None), residues: 0 loop : -1.93 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 239 TYR 0.016 0.002 TYR N 88 PHE 0.034 0.002 PHE E 116 TRP 0.014 0.001 TRP M 241 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 7582) covalent geometry : angle 0.70895 (10289) SS BOND : bond 0.20975 ( 1) SS BOND : angle 19.51012 ( 2) hydrogen bonds : bond 0.04514 ( 465) hydrogen bonds : angle 4.97108 ( 1392) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7398 (mm) cc_final: 0.7006 (mt) REVERT: E 87 ASN cc_start: 0.5280 (t0) cc_final: 0.4950 (t0) REVERT: F 61 MET cc_start: 0.7225 (mmm) cc_final: 0.6723 (mpp) REVERT: I 81 MET cc_start: 0.5587 (tpt) cc_final: 0.5347 (tpt) REVERT: J 111 GLU cc_start: 0.4560 (OUTLIER) cc_final: 0.3785 (tt0) REVERT: M 132 ASP cc_start: 0.7693 (m-30) cc_final: 0.7342 (m-30) REVERT: M 164 LEU cc_start: 0.8131 (mt) cc_final: 0.7909 (mt) REVERT: M 171 ASN cc_start: 0.8113 (t0) cc_final: 0.7886 (t0) REVERT: M 294 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7463 (tt) outliers start: 33 outliers final: 17 residues processed: 159 average time/residue: 0.0710 time to fit residues: 16.4505 Evaluate side-chains 123 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 0.0030 chunk 91 optimal weight: 0.0370 overall best weight: 0.1868 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.136739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 171)---------------| | r_work = 0.3974 r_free = 0.3974 target = 0.120668 restraints weight = 19964.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.120239 restraints weight = 16392.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120661 restraints weight = 12915.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121014 restraints weight = 11107.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.121038 restraints weight = 10175.825| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 7583 Z= 0.193 Angle : 0.674 26.895 10291 Z= 0.337 Chirality : 0.042 0.328 1286 Planarity : 0.004 0.041 1259 Dihedral : 5.498 48.433 1064 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 4.12 % Allowed : 19.81 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -2.28 (0.26), residues: 1015 helix: -1.46 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -0.80 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 239 TYR 0.011 0.001 TYR N 88 PHE 0.035 0.002 PHE D 107 TRP 0.010 0.001 TRP M 117 HIS 0.002 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7582) covalent geometry : angle 0.61918 (10289) SS BOND : bond 0.20147 ( 1) SS BOND : angle 19.03641 ( 2) hydrogen bonds : bond 0.03980 ( 465) hydrogen bonds : angle 4.37713 ( 1392) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7281 (mm) cc_final: 0.7017 (mt) REVERT: D 81 MET cc_start: 0.7457 (ttp) cc_final: 0.6928 (tmm) REVERT: D 113 ILE cc_start: 0.6914 (mm) cc_final: 0.6571 (mm) REVERT: F 61 MET cc_start: 0.7709 (mmm) cc_final: 0.7237 (mpp) REVERT: F 82 PHE cc_start: 0.6011 (m-10) cc_final: 0.5494 (m-10) REVERT: G 81 MET cc_start: 0.7107 (tpt) cc_final: 0.6303 (tmm) REVERT: G 116 PHE cc_start: 0.5589 (OUTLIER) cc_final: 0.4969 (m-80) REVERT: I 78 LEU cc_start: 0.6267 (pp) cc_final: 0.5271 (tt) REVERT: I 91 ARG cc_start: 0.6212 (mmm160) cc_final: 0.5698 (mmm160) REVERT: J 111 GLU cc_start: 0.4874 (OUTLIER) cc_final: 0.4320 (tt0) REVERT: J 116 PHE cc_start: 0.6328 (t80) cc_final: 0.6050 (t80) REVERT: M 171 ASN cc_start: 0.8133 (t0) cc_final: 0.7881 (t0) REVERT: M 294 LEU cc_start: 0.8051 (tt) cc_final: 0.7541 (tt) outliers start: 31 outliers final: 18 residues processed: 147 average time/residue: 0.0803 time to fit residues: 16.5673 Evaluate side-chains 119 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 281 LEU Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 37 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 90 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 1 optimal weight: 0.4980 chunk 60 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 182)---------------| | r_work = 0.3938 r_free = 0.3938 target = 0.118096 restraints weight = 20224.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 121)---------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115611 restraints weight = 21295.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.115849 restraints weight = 17398.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.115980 restraints weight = 15547.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.116236 restraints weight = 14234.898| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.197 7583 Z= 0.221 Angle : 0.725 26.493 10291 Z= 0.357 Chirality : 0.044 0.359 1286 Planarity : 0.004 0.044 1259 Dihedral : 5.587 48.387 1064 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 6.91 % Allowed : 17.95 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.58 (0.27), residues: 1015 helix: -0.91 (0.18), residues: 803 sheet: None (None), residues: 0 loop : -0.81 (0.50), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 232 TYR 0.009 0.001 TYR N 88 PHE 0.028 0.002 PHE D 107 TRP 0.007 0.001 TRP M 117 HIS 0.005 0.002 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 7582) covalent geometry : angle 0.67626 (10289) SS BOND : bond 0.19745 ( 1) SS BOND : angle 18.75370 ( 2) hydrogen bonds : bond 0.03940 ( 465) hydrogen bonds : angle 4.33714 ( 1392) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 107 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: C 61 MET cc_start: 0.8383 (mpp) cc_final: 0.7722 (mpp) REVERT: D 81 MET cc_start: 0.7377 (ttp) cc_final: 0.6816 (tmm) REVERT: D 110 THR cc_start: 0.5972 (m) cc_final: 0.5703 (p) REVERT: E 78 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6154 (tp) REVERT: F 61 MET cc_start: 0.7747 (mmm) cc_final: 0.7418 (mpp) REVERT: G 116 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.5206 (m-80) REVERT: H 61 MET cc_start: 0.6203 (mmm) cc_final: 0.5751 (mmm) REVERT: H 80 VAL cc_start: 0.7565 (OUTLIER) cc_final: 0.7359 (m) REVERT: I 71 LEU cc_start: 0.7129 (tt) cc_final: 0.6861 (mt) REVERT: I 91 ARG cc_start: 0.5916 (mmm160) cc_final: 0.5589 (mmm160) REVERT: J 60 LYS cc_start: 0.6872 (mtpt) cc_final: 0.6493 (mtpt) REVERT: J 111 GLU cc_start: 0.5215 (OUTLIER) cc_final: 0.4341 (tt0) REVERT: J 116 PHE cc_start: 0.6180 (t80) cc_final: 0.5950 (t80) REVERT: M 294 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7565 (tt) outliers start: 52 outliers final: 28 residues processed: 150 average time/residue: 0.0727 time to fit residues: 15.6784 Evaluate side-chains 131 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 98 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 72 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 99 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.131796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3924 r_free = 0.3924 target = 0.116916 restraints weight = 20096.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 104)---------------| | r_work = 0.3867 r_free = 0.3867 target = 0.114683 restraints weight = 20315.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.115309 restraints weight = 14979.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115945 restraints weight = 12319.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.116090 restraints weight = 10882.400| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.5274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 7583 Z= 0.205 Angle : 0.684 25.975 10291 Z= 0.337 Chirality : 0.042 0.337 1286 Planarity : 0.004 0.043 1259 Dihedral : 5.391 48.484 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 6.38 % Allowed : 20.74 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.00 (0.27), residues: 1015 helix: -0.51 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.58 (0.52), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.009 0.001 TYR N 88 PHE 0.025 0.002 PHE G 107 TRP 0.008 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 7582) covalent geometry : angle 0.63454 (10289) SS BOND : bond 0.19608 ( 1) SS BOND : angle 18.37626 ( 2) hydrogen bonds : bond 0.03799 ( 465) hydrogen bonds : angle 4.13719 ( 1392) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.260 Fit side-chains REVERT: B 95 ILE cc_start: 0.3936 (tt) cc_final: 0.3570 (mt) REVERT: C 61 MET cc_start: 0.8297 (mpp) cc_final: 0.7707 (mpp) REVERT: D 81 MET cc_start: 0.7262 (ttp) cc_final: 0.6780 (tmm) REVERT: D 110 THR cc_start: 0.6175 (m) cc_final: 0.5959 (p) REVERT: E 111 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6272 (mt-10) REVERT: F 115 LEU cc_start: 0.7188 (mm) cc_final: 0.6980 (mm) REVERT: G 81 MET cc_start: 0.6959 (tpt) cc_final: 0.6613 (tmm) REVERT: G 116 PHE cc_start: 0.5625 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: H 61 MET cc_start: 0.5948 (mmm) cc_final: 0.5475 (mmm) REVERT: H 82 PHE cc_start: 0.5423 (OUTLIER) cc_final: 0.4950 (m-10) REVERT: I 91 ARG cc_start: 0.5872 (mmm160) cc_final: 0.5483 (mmm160) REVERT: J 60 LYS cc_start: 0.6771 (mtpt) cc_final: 0.6508 (mtpt) REVERT: J 111 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4557 (tt0) REVERT: J 116 PHE cc_start: 0.6448 (t80) cc_final: 0.6221 (t80) REVERT: M 294 LEU cc_start: 0.8127 (tt) cc_final: 0.7658 (tt) outliers start: 48 outliers final: 32 residues processed: 148 average time/residue: 0.0693 time to fit residues: 15.0269 Evaluate side-chains 136 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 37 optimal weight: 0.0770 chunk 33 optimal weight: 0.5980 chunk 75 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.130906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.117756 restraints weight = 19964.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116588 restraints weight = 20867.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.114766 restraints weight = 22228.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.114971 restraints weight = 21063.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115214 restraints weight = 17342.377| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.5543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 7583 Z= 0.204 Angle : 0.689 25.891 10291 Z= 0.337 Chirality : 0.041 0.247 1286 Planarity : 0.004 0.047 1259 Dihedral : 5.337 48.155 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.26 % Rotamer: Outliers : 6.78 % Allowed : 21.01 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.77 (0.27), residues: 1015 helix: -0.27 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.87 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.010 0.001 TYR N 88 PHE 0.028 0.002 PHE G 107 TRP 0.009 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7582) covalent geometry : angle 0.63958 (10289) SS BOND : bond 0.19341 ( 1) SS BOND : angle 18.34286 ( 2) hydrogen bonds : bond 0.03728 ( 465) hydrogen bonds : angle 4.10307 ( 1392) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.304 Fit side-chains REVERT: B 95 ILE cc_start: 0.4729 (tt) cc_final: 0.4236 (mt) REVERT: C 61 MET cc_start: 0.8267 (mpp) cc_final: 0.7723 (mpp) REVERT: D 81 MET cc_start: 0.7054 (ttp) cc_final: 0.6719 (tmm) REVERT: F 61 MET cc_start: 0.7135 (mmt) cc_final: 0.6765 (mpp) REVERT: G 81 MET cc_start: 0.7006 (tpt) cc_final: 0.6473 (tmm) REVERT: G 116 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5305 (m-80) REVERT: H 61 MET cc_start: 0.5574 (mmm) cc_final: 0.5138 (mmm) REVERT: H 80 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7463 (m) REVERT: H 82 PHE cc_start: 0.5344 (OUTLIER) cc_final: 0.4762 (m-10) REVERT: H 116 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5446 (m-80) REVERT: I 71 LEU cc_start: 0.7090 (tt) cc_final: 0.6815 (mt) REVERT: I 91 ARG cc_start: 0.5782 (mmm160) cc_final: 0.5197 (mmp-170) REVERT: J 111 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.4470 (tt0) REVERT: M 294 LEU cc_start: 0.8137 (tt) cc_final: 0.7844 (tt) outliers start: 51 outliers final: 35 residues processed: 152 average time/residue: 0.0682 time to fit residues: 15.0894 Evaluate side-chains 137 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.0370 chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 0.1980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.129623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112739 restraints weight = 20128.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.113396 restraints weight = 15127.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113826 restraints weight = 12337.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114016 restraints weight = 10821.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114030 restraints weight = 10092.134| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.194 7583 Z= 0.212 Angle : 0.703 26.180 10291 Z= 0.344 Chirality : 0.042 0.243 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.384 47.567 1064 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 7.18 % Allowed : 20.61 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.64 (0.28), residues: 1015 helix: -0.17 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.84 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 133 TYR 0.010 0.001 TYR N 88 PHE 0.023 0.002 PHE A 116 TRP 0.010 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 7582) covalent geometry : angle 0.65342 (10289) SS BOND : bond 0.19399 ( 1) SS BOND : angle 18.55781 ( 2) hydrogen bonds : bond 0.03786 ( 465) hydrogen bonds : angle 4.17156 ( 1392) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 95 ILE cc_start: 0.4991 (tt) cc_final: 0.4627 (mt) REVERT: C 61 MET cc_start: 0.8461 (mpp) cc_final: 0.7742 (mpp) REVERT: D 81 MET cc_start: 0.7257 (ttp) cc_final: 0.6796 (tmm) REVERT: F 61 MET cc_start: 0.7535 (mmt) cc_final: 0.7177 (mpp) REVERT: G 81 MET cc_start: 0.7111 (tpt) cc_final: 0.6572 (tmm) REVERT: G 116 PHE cc_start: 0.5773 (OUTLIER) cc_final: 0.5333 (m-80) REVERT: H 61 MET cc_start: 0.5618 (mmm) cc_final: 0.5278 (mmm) REVERT: H 80 VAL cc_start: 0.7774 (OUTLIER) cc_final: 0.7502 (m) REVERT: H 82 PHE cc_start: 0.5389 (OUTLIER) cc_final: 0.4884 (m-10) REVERT: H 116 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5647 (m-80) REVERT: I 71 LEU cc_start: 0.7214 (tt) cc_final: 0.6894 (mt) REVERT: J 111 GLU cc_start: 0.5317 (OUTLIER) cc_final: 0.5073 (tp30) REVERT: M 294 LEU cc_start: 0.8184 (tt) cc_final: 0.7900 (tt) outliers start: 54 outliers final: 42 residues processed: 146 average time/residue: 0.0693 time to fit residues: 14.7594 Evaluate side-chains 142 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 95 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 66 optimal weight: 0.0470 chunk 18 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 89 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.0980 chunk 80 optimal weight: 0.8980 overall best weight: 0.1686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.132508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 156)---------------| | r_work = 0.3894 r_free = 0.3894 target = 0.116179 restraints weight = 20197.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.116399 restraints weight = 17416.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117071 restraints weight = 13170.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.117198 restraints weight = 11196.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117382 restraints weight = 10102.056| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 7583 Z= 0.184 Angle : 0.660 25.610 10291 Z= 0.320 Chirality : 0.040 0.233 1286 Planarity : 0.003 0.048 1259 Dihedral : 5.095 48.679 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.76 % Favored : 97.14 % Rotamer: Outliers : 5.72 % Allowed : 22.07 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.22 (0.28), residues: 1015 helix: 0.11 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.64 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 239 TYR 0.011 0.001 TYR N 88 PHE 0.032 0.001 PHE F 116 TRP 0.009 0.001 TRP M 215 HIS 0.003 0.001 HIS M 252 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7582) covalent geometry : angle 0.60981 (10289) SS BOND : bond 0.19557 ( 1) SS BOND : angle 18.14066 ( 2) hydrogen bonds : bond 0.03454 ( 465) hydrogen bonds : angle 3.86745 ( 1392) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7208 (tmt) cc_final: 0.6936 (tmt) REVERT: E 97 LYS cc_start: 0.4614 (mmtm) cc_final: 0.4383 (tppt) REVERT: F 60 LYS cc_start: 0.6799 (tppt) cc_final: 0.6080 (ttmt) REVERT: G 81 MET cc_start: 0.7020 (tpt) cc_final: 0.6643 (tmm) REVERT: G 116 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5293 (m-80) REVERT: H 61 MET cc_start: 0.5673 (mmm) cc_final: 0.5275 (mmm) REVERT: H 80 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7309 (m) REVERT: H 82 PHE cc_start: 0.4948 (OUTLIER) cc_final: 0.4399 (m-10) REVERT: I 71 LEU cc_start: 0.7144 (tt) cc_final: 0.6849 (mt) REVERT: J 82 PHE cc_start: 0.7965 (m-80) cc_final: 0.7350 (t80) REVERT: J 111 GLU cc_start: 0.5221 (OUTLIER) cc_final: 0.4902 (mm-30) REVERT: M 294 LEU cc_start: 0.8108 (tt) cc_final: 0.7825 (tt) REVERT: M 316 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7155 (pt) outliers start: 43 outliers final: 32 residues processed: 141 average time/residue: 0.0646 time to fit residues: 13.3732 Evaluate side-chains 133 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 85 optimal weight: 0.0980 chunk 90 optimal weight: 0.2980 chunk 81 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.130261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3871 r_free = 0.3871 target = 0.114025 restraints weight = 19955.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114202 restraints weight = 15218.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.114591 restraints weight = 12059.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.114615 restraints weight = 10533.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114835 restraints weight = 10280.181| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 7583 Z= 0.210 Angle : 0.707 25.552 10291 Z= 0.344 Chirality : 0.042 0.247 1286 Planarity : 0.004 0.046 1259 Dihedral : 5.243 48.407 1064 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 6.25 % Allowed : 22.34 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.29 (0.28), residues: 1015 helix: 0.09 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.78 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 91 TYR 0.009 0.001 TYR D 102 PHE 0.031 0.002 PHE F 116 TRP 0.009 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 7582) covalent geometry : angle 0.66054 (10289) SS BOND : bond 0.19659 ( 1) SS BOND : angle 18.09449 ( 2) hydrogen bonds : bond 0.03711 ( 465) hydrogen bonds : angle 4.04153 ( 1392) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.281 Fit side-chains REVERT: D 113 ILE cc_start: 0.6133 (mt) cc_final: 0.5845 (tt) REVERT: D 116 PHE cc_start: 0.5628 (m-80) cc_final: 0.5413 (m-80) REVERT: E 97 LYS cc_start: 0.4410 (mmtm) cc_final: 0.4108 (tppt) REVERT: F 60 LYS cc_start: 0.6771 (tppt) cc_final: 0.6234 (ttmm) REVERT: G 81 MET cc_start: 0.7114 (tpt) cc_final: 0.6761 (tmm) REVERT: G 116 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5467 (m-80) REVERT: H 61 MET cc_start: 0.5466 (mmm) cc_final: 0.5189 (mmm) REVERT: H 80 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7441 (m) REVERT: H 82 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: H 116 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5651 (m-80) REVERT: I 71 LEU cc_start: 0.7171 (tt) cc_final: 0.6881 (mt) REVERT: I 91 ARG cc_start: 0.5869 (mmm160) cc_final: 0.5622 (mmp-170) REVERT: M 294 LEU cc_start: 0.8168 (tt) cc_final: 0.7886 (tt) outliers start: 47 outliers final: 37 residues processed: 140 average time/residue: 0.0645 time to fit residues: 13.3438 Evaluate side-chains 139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.2980 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.127400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.114515 restraints weight = 20090.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 166)---------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112318 restraints weight = 24495.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.112216 restraints weight = 22658.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.112374 restraints weight = 16778.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.112420 restraints weight = 15384.268| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.196 7583 Z= 0.251 Angle : 0.790 26.037 10291 Z= 0.383 Chirality : 0.045 0.240 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.642 47.771 1064 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 6.25 % Allowed : 23.40 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.51 (0.27), residues: 1015 helix: -0.12 (0.19), residues: 785 sheet: None (None), residues: 0 loop : -0.61 (0.47), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 145 TYR 0.010 0.002 TYR D 102 PHE 0.030 0.002 PHE F 116 TRP 0.012 0.002 TRP M 215 HIS 0.004 0.002 HIS N 97 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7582) covalent geometry : angle 0.74699 (10289) SS BOND : bond 0.19576 ( 1) SS BOND : angle 18.46838 ( 2) hydrogen bonds : bond 0.04160 ( 465) hydrogen bonds : angle 4.40010 ( 1392) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.454 Fit side-chains REVERT: F 60 LYS cc_start: 0.6463 (tppt) cc_final: 0.5985 (ttmm) REVERT: F 61 MET cc_start: 0.7484 (mpp) cc_final: 0.7143 (mmm) REVERT: G 116 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.5406 (m-80) REVERT: H 80 VAL cc_start: 0.7725 (OUTLIER) cc_final: 0.7482 (m) REVERT: H 82 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4916 (m-80) REVERT: H 116 PHE cc_start: 0.6039 (OUTLIER) cc_final: 0.5574 (m-80) REVERT: I 71 LEU cc_start: 0.7125 (tt) cc_final: 0.6835 (mt) REVERT: I 91 ARG cc_start: 0.5946 (mmm160) cc_final: 0.5710 (mmp-170) REVERT: M 294 LEU cc_start: 0.8137 (tt) cc_final: 0.7876 (tt) REVERT: M 316 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7337 (pt) outliers start: 47 outliers final: 39 residues processed: 146 average time/residue: 0.0702 time to fit residues: 14.9747 Evaluate side-chains 147 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 103 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 95 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 18 optimal weight: 0.0570 chunk 93 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 81 optimal weight: 0.0050 chunk 24 optimal weight: 0.9990 chunk 84 optimal weight: 0.2980 chunk 79 optimal weight: 0.0770 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.1980 overall best weight: 0.0708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN N 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.133111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.119753 restraints weight = 19958.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.119367 restraints weight = 24010.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.120195 restraints weight = 18129.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.120183 restraints weight = 13726.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.120841 restraints weight = 12276.320| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 7583 Z= 0.183 Angle : 0.697 25.911 10291 Z= 0.337 Chirality : 0.041 0.277 1286 Planarity : 0.003 0.045 1259 Dihedral : 5.121 47.903 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 5.19 % Allowed : 24.20 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: 0.06 (0.28), residues: 1015 helix: 0.30 (0.19), residues: 787 sheet: None (None), residues: 0 loop : -0.43 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.015 0.001 TYR N 88 PHE 0.039 0.002 PHE I 107 TRP 0.011 0.001 TRP M 117 HIS 0.002 0.001 HIS M 248 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7582) covalent geometry : angle 0.64828 (10289) SS BOND : bond 0.19608 ( 1) SS BOND : angle 18.35955 ( 2) hydrogen bonds : bond 0.03424 ( 465) hydrogen bonds : angle 3.89924 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1815.68 seconds wall clock time: 31 minutes 56.32 seconds (1916.32 seconds total)