Starting phenix.real_space_refine on Fri Oct 23 00:48:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f36_4176/10_2026/6f36_4176.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f36_4176/10_2026/6f36_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_4176/10_2026/6f36_4176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f36_4176/10_2026/6f36_4176.map" model { file = "/net/cci-nas-00/data/ceres_data/6f36_4176/10_2026/6f36_4176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f36_4176/10_2026/6f36_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-2.3rc1-6221/lib/python3.11/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: 1.43, per 1000 atoms: 0.19 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=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 373.6 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: 0.17 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: 0.95 Time building geometry restraints manager: 0.77 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: 4012 14.81 - 29.61: 259 29.61 - 44.42: 74 44.42 - 59.22: 3 59.22 - 74.03: 2 Dihedral angle restraints: 4350 sinusoidal: 1480 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 4347 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: 2505 2.82 - 3.34: 7174 3.34 - 3.86: 11840 3.86 - 4.38: 15001 4.38 - 4.90: 23179 Nonbonded interactions: 59699 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 59694 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: 7.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.490 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 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 : 0.010 0.394 7582 Z= 0.487 Angle : 1.135 10.462 10289 Z= 0.567 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/Z covalent geometry : bond 0.00984 / 0.49 ( 7582) covalent geometry : angle 1.13476 / 0.57 (10289) hydrogen bonds : bond 0.29303 / 19.50 ( 465) hydrogen bonds : angle 10.28637 / 7.12 ( 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 : 0.260 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: 0.6288 (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: 0.0677 time to fit residues: 21.6170 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 : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] 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... A 87 ASN M 243 ASN N 93 GLN N 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 157)---------------| | r_work = 0.4039 r_free = 0.4039 target = 0.124664 restraints weight = 20313.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 99)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.122616 restraints weight = 25959.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.121983 restraints weight = 19793.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.122365 restraints weight = 16074.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.122703 restraints weight = 13999.484| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7582 Z= 0.147 Angle : 0.708 9.279 10289 Z= 0.350 Chirality : 0.041 0.198 1286 Planarity : 0.005 0.050 1259 Dihedral : 6.013 19.238 1064 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.26 % Allowed : 17.42 % Favored : 78.32 % 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: -4.14 (0.22), residues: 1015 helix: -2.65 (0.14), residues: 811 sheet: None (None), residues: 0 loop : -1.96 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 239 TYR 0.016 0.002 TYR N 88 PHE 0.035 0.002 PHE E 116 TRP 0.013 0.001 TRP M 117 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 7582) covalent geometry : angle 0.70757 / 0.35 (10289) hydrogen bonds : bond 0.04710 / 3.07 ( 465) hydrogen bonds : angle 4.98653 / 3.50 ( 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 168 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7441 (mm) cc_final: 0.7073 (mt) REVERT: C 61 MET cc_start: 0.8175 (mpp) cc_final: 0.7930 (mpp) REVERT: C 84 SER cc_start: 0.8233 (m) cc_final: 0.8032 (t) REVERT: D 109 LEU cc_start: 0.5769 (mt) cc_final: 0.5532 (mt) REVERT: E 87 ASN cc_start: 0.5263 (t0) cc_final: 0.4907 (t0) REVERT: F 61 MET cc_start: 0.7299 (mmm) cc_final: 0.6608 (mpp) REVERT: J 111 GLU cc_start: 0.4534 (OUTLIER) cc_final: 0.3746 (tt0) REVERT: M 132 ASP cc_start: 0.7673 (m-30) cc_final: 0.7326 (m-30) REVERT: M 164 LEU cc_start: 0.8074 (mt) cc_final: 0.7843 (mt) REVERT: M 171 ASN cc_start: 0.8059 (t0) cc_final: 0.7835 (t0) REVERT: M 294 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7381 (tt) outliers start: 32 outliers final: 17 residues processed: 156 average time/residue: 0.0643 time to fit residues: 14.7219 Evaluate side-chains 122 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: [20, 31, 25, 62, 94, 98, 34, 44, 24, 73, 91] chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 44 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 91 optimal weight: 0.0020 overall best weight: 0.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 252 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.136693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.121943 restraints weight = 20049.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.121839 restraints weight = 20507.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.122452 restraints weight = 17200.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.122172 restraints weight = 13922.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.122360 restraints weight = 12834.627| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7582 Z= 0.130 Angle : 0.613 8.216 10289 Z= 0.305 Chirality : 0.041 0.354 1286 Planarity : 0.004 0.043 1259 Dihedral : 5.423 17.220 1064 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.52 % Allowed : 19.81 % Favored : 75.66 % 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: -2.38 (0.25), residues: 1015 helix: -1.53 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 239 TYR 0.036 0.002 TYR J 102 PHE 0.027 0.002 PHE D 107 TRP 0.010 0.001 TRP M 117 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 7582) covalent geometry : angle 0.61321 / 0.31 (10289) hydrogen bonds : bond 0.04017 / 2.61 ( 465) hydrogen bonds : angle 4.32949 / 3.07 ( 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 160 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7259 (mm) cc_final: 0.6991 (mt) REVERT: D 81 MET cc_start: 0.7251 (ttp) cc_final: 0.6865 (tmm) REVERT: F 61 MET cc_start: 0.7530 (mmm) cc_final: 0.7267 (mpp) REVERT: G 116 PHE cc_start: 0.5556 (OUTLIER) cc_final: 0.4946 (m-80) REVERT: I 78 LEU cc_start: 0.6178 (pp) cc_final: 0.5203 (tt) REVERT: I 91 ARG cc_start: 0.5825 (mmm160) cc_final: 0.5424 (mmm160) REVERT: J 111 GLU cc_start: 0.4998 (OUTLIER) cc_final: 0.4417 (tt0) REVERT: J 116 PHE cc_start: 0.6153 (t80) cc_final: 0.5899 (t80) REVERT: M 132 ASP cc_start: 0.7554 (m-30) cc_final: 0.7202 (m-30) REVERT: M 171 ASN cc_start: 0.8191 (t0) cc_final: 0.7940 (t0) REVERT: M 294 LEU cc_start: 0.8051 (tt) cc_final: 0.7610 (tt) outliers start: 34 outliers final: 19 residues processed: 151 average time/residue: 0.0721 time to fit residues: 15.5076 Evaluate side-chains 123 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 238 VAL Chi-restraints excluded: chain M residue 271 VAL 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: [70, 20, 30, 88, 37, 26, 90, 15, 78, 1, 60] chunk 70 optimal weight: 0.0020 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 90 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 1 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 overall best weight: 0.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.136099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 130)---------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121188 restraints weight = 20291.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 103)---------------| | r_work = 0.3934 r_free = 0.3934 target = 0.118815 restraints weight = 21851.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119570 restraints weight = 16143.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119570 restraints weight = 13142.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.119570 restraints weight = 13142.527| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7582 Z= 0.124 Angle : 0.600 7.421 10289 Z= 0.292 Chirality : 0.041 0.348 1286 Planarity : 0.004 0.038 1259 Dihedral : 5.174 16.945 1064 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.72 % Allowed : 20.35 % Favored : 73.94 % 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: -1.42 (0.27), residues: 1015 helix: -0.84 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 239 TYR 0.032 0.001 TYR J 102 PHE 0.025 0.001 PHE F 116 TRP 0.008 0.001 TRP M 117 HIS 0.002 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7582) covalent geometry : angle 0.60003 / 0.29 (10289) hydrogen bonds : bond 0.03609 / 2.35 ( 465) hydrogen bonds : angle 3.99768 / 2.85 ( 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 150 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7729 (mm) cc_final: 0.7497 (mt) REVERT: C 81 MET cc_start: 0.7147 (tmt) cc_final: 0.6723 (tmt) REVERT: D 81 MET cc_start: 0.7131 (ttp) cc_final: 0.6662 (tmm) REVERT: D 110 THR cc_start: 0.6189 (m) cc_final: 0.5918 (p) REVERT: E 78 LEU cc_start: 0.6396 (OUTLIER) cc_final: 0.6117 (tp) REVERT: E 105 LEU cc_start: 0.3682 (tt) cc_final: 0.1341 (mt) REVERT: F 61 MET cc_start: 0.7830 (mmm) cc_final: 0.7366 (mpp) REVERT: G 116 PHE cc_start: 0.5523 (OUTLIER) cc_final: 0.5044 (m-80) REVERT: I 71 LEU cc_start: 0.7014 (tt) cc_final: 0.6726 (mt) REVERT: I 91 ARG cc_start: 0.5988 (mmm160) cc_final: 0.5607 (mmm160) REVERT: M 171 ASN cc_start: 0.8098 (t0) cc_final: 0.7837 (t0) REVERT: M 294 LEU cc_start: 0.8104 (tt) cc_final: 0.7577 (tt) outliers start: 43 outliers final: 26 residues processed: 143 average time/residue: 0.0686 time to fit residues: 14.1192 Evaluate side-chains 125 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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 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 125 LEU Chi-restraints excluded: chain I residue 80 VAL 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 110 LEU Chi-restraints excluded: chain M residue 193 THR 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 N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [65, 63, 10, 75, 6, 72, 45, 40, 99, 62, 67] chunk 65 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 0.0770 chunk 62 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 overall best weight: 0.2736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.133442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 201)---------------| | r_work = 0.3914 r_free = 0.3914 target = 0.117146 restraints weight = 20163.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 77)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.117059 restraints weight = 15383.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.117439 restraints weight = 12489.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117740 restraints weight = 10893.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117741 restraints weight = 10052.053| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7582 Z= 0.138 Angle : 0.603 7.545 10289 Z= 0.294 Chirality : 0.041 0.310 1286 Planarity : 0.004 0.040 1259 Dihedral : 5.080 16.516 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.32 % Allowed : 21.01 % Favored : 73.67 % 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: -0.92 (0.27), residues: 1015 helix: -0.45 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -0.55 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.026 0.001 TYR J 102 PHE 0.021 0.002 PHE A 116 TRP 0.008 0.001 TRP M 117 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 7582) covalent geometry : angle 0.60316 / 0.29 (10289) hydrogen bonds : bond 0.03612 / 2.36 ( 465) hydrogen bonds : angle 3.90573 / 2.78 ( 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 152 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 112 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7272 (tmt) cc_final: 0.6827 (tmt) REVERT: D 81 MET cc_start: 0.7042 (ttp) cc_final: 0.6736 (tmm) REVERT: D 110 THR cc_start: 0.6057 (m) cc_final: 0.5827 (p) REVERT: E 71 LEU cc_start: 0.7894 (mm) cc_final: 0.7548 (mt) REVERT: E 78 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6106 (tp) REVERT: E 105 LEU cc_start: 0.4326 (OUTLIER) cc_final: 0.3873 (tp) REVERT: F 61 MET cc_start: 0.7539 (mmm) cc_final: 0.6843 (mpp) REVERT: G 116 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.5228 (m-80) REVERT: H 61 MET cc_start: 0.6287 (mmm) cc_final: 0.5614 (mmm) REVERT: I 91 ARG cc_start: 0.5931 (mmm160) cc_final: 0.5478 (mmm160) REVERT: M 294 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7567 (tt) outliers start: 40 outliers final: 25 residues processed: 141 average time/residue: 0.0586 time to fit residues: 12.0463 Evaluate side-chains 130 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.281 ------------------------------------------------------------------------------- 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 105 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 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 82 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 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 294 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [51, 14, 9, 74, 37, 33, 75, 44, 22, 54, 38] chunk 51 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 37 optimal weight: 0.0030 chunk 33 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4156 r_free = 0.4156 target = 0.133778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 148)---------------| | r_work = 0.3930 r_free = 0.3930 target = 0.117861 restraints weight = 20145.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.117750 restraints weight = 14958.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118100 restraints weight = 12127.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.118268 restraints weight = 10617.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.118280 restraints weight = 9951.187| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7582 Z= 0.126 Angle : 0.593 10.109 10289 Z= 0.286 Chirality : 0.039 0.237 1286 Planarity : 0.003 0.044 1259 Dihedral : 4.899 16.389 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.32 % Allowed : 22.21 % Favored : 72.47 % 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: -0.52 (0.28), residues: 1015 helix: -0.17 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.41 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.025 0.001 TYR J 102 PHE 0.022 0.001 PHE D 107 TRP 0.007 0.001 TRP M 117 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7582) covalent geometry : angle 0.59342 / 0.29 (10289) hydrogen bonds : bond 0.03510 / 2.27 ( 465) hydrogen bonds : angle 3.76203 / 2.68 ( 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 151 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7317 (tmt) cc_final: 0.6865 (tmt) REVERT: D 81 MET cc_start: 0.7067 (ttp) cc_final: 0.6706 (tmm) REVERT: E 105 LEU cc_start: 0.4026 (tt) cc_final: 0.3599 (tp) REVERT: F 61 MET cc_start: 0.7482 (mmm) cc_final: 0.6691 (mpp) REVERT: F 115 LEU cc_start: 0.7052 (mm) cc_final: 0.6810 (mm) REVERT: G 116 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5415 (m-80) REVERT: I 71 LEU cc_start: 0.7063 (tt) cc_final: 0.6790 (mt) REVERT: I 91 ARG cc_start: 0.5891 (mmm160) cc_final: 0.5410 (mmm160) REVERT: J 82 PHE cc_start: 0.8018 (m-80) cc_final: 0.7260 (t80) REVERT: M 294 LEU cc_start: 0.8086 (tt) cc_final: 0.7794 (tt) outliers start: 40 outliers final: 28 residues processed: 146 average time/residue: 0.0624 time to fit residues: 13.3968 Evaluate side-chains 129 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 B residue 125 LEU Chi-restraints excluded: chain C residue 116 PHE 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 119 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 55 VAL Chi-restraints excluded: chain H residue 82 PHE 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 110 LEU 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 84 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [13, 16, 80, 72, 38, 99, 78, 88, 74, 4, 76] chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4104 r_free = 0.4104 target = 0.129600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.114772 restraints weight = 20183.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.114663 restraints weight = 19883.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115587 restraints weight = 15424.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.115267 restraints weight = 12117.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.115376 restraints weight = 11800.788| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7582 Z= 0.183 Angle : 0.700 9.923 10289 Z= 0.334 Chirality : 0.043 0.265 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.272 18.024 1064 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.72 % Allowed : 22.34 % Favored : 71.94 % 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: -0.64 (0.27), residues: 1015 helix: -0.22 (0.19), residues: 803 sheet: None (None), residues: 0 loop : -0.58 (0.50), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 133 TYR 0.023 0.002 TYR J 102 PHE 0.031 0.002 PHE F 116 TRP 0.010 0.002 TRP M 215 HIS 0.005 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 7582) covalent geometry : angle 0.70008 / 0.33 (10289) hydrogen bonds : bond 0.03932 / 2.57 ( 465) hydrogen bonds : angle 4.15615 / 2.94 ( 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 150 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 0.293 Fit side-chains REVERT: B 95 ILE cc_start: 0.4492 (tt) cc_final: 0.4192 (mt) REVERT: F 61 MET cc_start: 0.7328 (mmm) cc_final: 0.6901 (mpp) REVERT: G 116 PHE cc_start: 0.5652 (OUTLIER) cc_final: 0.5203 (m-80) REVERT: H 61 MET cc_start: 0.6359 (mmm) cc_final: 0.5625 (mmm) REVERT: H 82 PHE cc_start: 0.5397 (OUTLIER) cc_final: 0.4774 (m-10) REVERT: H 116 PHE cc_start: 0.5779 (OUTLIER) cc_final: 0.5391 (m-80) REVERT: I 71 LEU cc_start: 0.7041 (tt) cc_final: 0.6706 (mt) REVERT: M 294 LEU cc_start: 0.8195 (tt) cc_final: 0.7889 (tt) outliers start: 43 outliers final: 33 residues processed: 144 average time/residue: 0.0664 time to fit residues: 14.0807 Evaluate side-chains 132 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 96 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU 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 78 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 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 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 84 SER Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [83, 57, 66, 18, 32, 93, 89, 56, 52, 51, 80] chunk 83 optimal weight: 0.4980 chunk 57 optimal weight: 0.0770 chunk 66 optimal weight: 0.1980 chunk 18 optimal weight: 0.0050 chunk 32 optimal weight: 0.8980 chunk 93 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4132 r_free = 0.4132 target = 0.131781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 163)---------------| | r_work = 0.3886 r_free = 0.3886 target = 0.115562 restraints weight = 20289.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.115886 restraints weight = 15480.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.116308 restraints weight = 12289.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.116685 restraints weight = 10657.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.116717 restraints weight = 9735.357| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7582 Z= 0.133 Angle : 0.648 11.480 10289 Z= 0.305 Chirality : 0.040 0.204 1286 Planarity : 0.004 0.047 1259 Dihedral : 5.039 17.228 1064 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.85 % Allowed : 22.74 % Favored : 71.41 % 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: -0.43 (0.27), residues: 1015 helix: -0.03 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.76 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 239 TYR 0.024 0.001 TYR J 102 PHE 0.034 0.002 PHE G 107 TRP 0.010 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7582) covalent geometry : angle 0.64759 / 0.31 (10289) hydrogen bonds : bond 0.03601 / 2.35 ( 465) hydrogen bonds : angle 3.86982 / 2.71 ( 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: 44 poor density : 105 time to evaluate : 0.274 Fit side-chains REVERT: B 95 ILE cc_start: 0.4776 (tt) cc_final: 0.4486 (mt) REVERT: C 81 MET cc_start: 0.7298 (tmt) cc_final: 0.6852 (tmt) REVERT: E 111 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6266 (mt-10) REVERT: F 61 MET cc_start: 0.7342 (mmm) cc_final: 0.6566 (mpp) REVERT: G 116 PHE cc_start: 0.5953 (OUTLIER) cc_final: 0.5556 (m-80) REVERT: H 61 MET cc_start: 0.6606 (mmm) cc_final: 0.5945 (mmm) REVERT: H 116 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.5642 (m-80) REVERT: I 71 LEU cc_start: 0.7194 (tt) cc_final: 0.6910 (mt) REVERT: J 82 PHE cc_start: 0.8098 (m-80) cc_final: 0.7332 (t80) REVERT: M 294 LEU cc_start: 0.8112 (tt) cc_final: 0.7817 (tt) outliers start: 44 outliers final: 37 residues processed: 142 average time/residue: 0.0681 time to fit residues: 14.1234 Evaluate side-chains 142 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 103 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL 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 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU 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 78 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 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 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 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 87 LEU 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: [33, 79, 85, 90, 81, 32, 36, 65, 62, 8, 2] chunk 33 optimal weight: 0.5980 chunk 79 optimal weight: 0.2980 chunk 85 optimal weight: 0.0980 chunk 90 optimal weight: 0.2980 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4107 r_free = 0.4107 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 142)---------------| | r_work = 0.3854 r_free = 0.3854 target = 0.113587 restraints weight = 19988.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.114142 restraints weight = 14279.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.114383 restraints weight = 12201.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114888 restraints weight = 10770.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114888 restraints weight = 9808.623| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7582 Z= 0.159 Angle : 0.668 9.941 10289 Z= 0.318 Chirality : 0.042 0.219 1286 Planarity : 0.004 0.045 1259 Dihedral : 5.149 16.514 1064 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.52 % Allowed : 21.68 % Favored : 71.81 % 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: -0.57 (0.27), residues: 1015 helix: -0.10 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.90 (0.47), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 239 TYR 0.022 0.002 TYR J 102 PHE 0.037 0.002 PHE G 107 TRP 0.010 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 7582) covalent geometry : angle 0.66810 / 0.32 (10289) hydrogen bonds : bond 0.03708 / 2.42 ( 465) hydrogen bonds : angle 3.99894 / 2.83 ( 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 154 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.255 Fit side-chains REVERT: C 81 MET cc_start: 0.7319 (tmt) cc_final: 0.6917 (tmt) REVERT: E 97 LYS cc_start: 0.4924 (mmtm) cc_final: 0.4510 (tppt) REVERT: F 61 MET cc_start: 0.7352 (mmm) cc_final: 0.6806 (mpp) REVERT: G 116 PHE cc_start: 0.5856 (OUTLIER) cc_final: 0.5487 (m-80) REVERT: H 61 MET cc_start: 0.6947 (mmm) cc_final: 0.6448 (mmm) REVERT: H 116 PHE cc_start: 0.5843 (OUTLIER) cc_final: 0.5410 (m-80) REVERT: I 71 LEU cc_start: 0.7230 (tt) cc_final: 0.6865 (mt) REVERT: M 294 LEU cc_start: 0.8134 (tt) cc_final: 0.7852 (tt) outliers start: 49 outliers final: 40 residues processed: 145 average time/residue: 0.0598 time to fit residues: 12.7993 Evaluate side-chains 140 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 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 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 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 78 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 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 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 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 265 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 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: [18, 41, 8, 43, 93, 48, 86, 37, 53, 29, 42] chunk 18 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 93 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 chunk 29 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4093 r_free = 0.4093 target = 0.129229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3855 r_free = 0.3855 target = 0.113185 restraints weight = 20161.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113487 restraints weight = 14414.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113851 restraints weight = 11757.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.113859 restraints weight = 10279.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.113992 restraints weight = 10158.062| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.6414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7582 Z= 0.170 Angle : 0.696 12.549 10289 Z= 0.330 Chirality : 0.043 0.309 1286 Planarity : 0.004 0.045 1259 Dihedral : 5.249 17.309 1064 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.25 % Allowed : 23.14 % Favored : 70.61 % 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: -0.68 (0.27), residues: 1015 helix: -0.18 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -0.93 (0.47), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 91 TYR 0.021 0.002 TYR J 102 PHE 0.028 0.002 PHE F 116 TRP 0.012 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 ( 7582) covalent geometry : angle 0.69632 / 0.33 (10289) hydrogen bonds : bond 0.03843 / 2.50 ( 465) hydrogen bonds : angle 4.06238 / 2.87 ( 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 145 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 98 time to evaluate : 0.314 Fit side-chains REVERT: C 81 MET cc_start: 0.7266 (tmt) cc_final: 0.6799 (tmt) REVERT: E 97 LYS cc_start: 0.4606 (mmtm) cc_final: 0.4269 (tppt) REVERT: F 60 LYS cc_start: 0.6933 (tppt) cc_final: 0.6456 (tptp) REVERT: F 61 MET cc_start: 0.7606 (mmm) cc_final: 0.6933 (mpp) REVERT: H 61 MET cc_start: 0.6725 (mmm) cc_final: 0.6324 (mmm) REVERT: H 116 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: I 71 LEU cc_start: 0.7230 (tt) cc_final: 0.6928 (mt) REVERT: M 294 LEU cc_start: 0.8160 (tt) cc_final: 0.7861 (tt) outliers start: 47 outliers final: 43 residues processed: 138 average time/residue: 0.0682 time to fit residues: 13.9341 Evaluate side-chains 141 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 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 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 78 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 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL 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 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 265 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 79 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 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: [18, 93, 56, 0, 76, 81, 24, 84, 79, 50, 73] chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 0.1980 chunk 56 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.0050 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 92 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 = 0.4089 r_free = 0.4089 target = 0.128952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 176)---------------| | r_work = 0.3860 r_free = 0.3860 target = 0.113138 restraints weight = 20016.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.112989 restraints weight = 14994.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.113334 restraints weight = 11998.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113644 restraints weight = 10509.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113644 restraints weight = 9637.719| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.6573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7582 Z= 0.171 Angle : 0.688 10.213 10289 Z= 0.329 Chirality : 0.044 0.279 1286 Planarity : 0.004 0.043 1259 Dihedral : 5.293 17.160 1064 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.25 % Allowed : 23.01 % Favored : 70.74 % 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: -0.68 (0.27), residues: 1015 helix: -0.17 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.99 (0.46), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 91 TYR 0.024 0.002 TYR J 102 PHE 0.034 0.002 PHE I 107 TRP 0.011 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7582) covalent geometry : angle 0.68782 / 0.33 (10289) hydrogen bonds : bond 0.03806 / 2.48 ( 465) hydrogen bonds : angle 4.12625 / 2.92 ( 1392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1713.69 seconds wall clock time: 30 minutes 10.66 seconds (1810.66 seconds total)