Starting phenix.real_space_refine on Wed Mar 12 05:31:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.cif Found real_map, /net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.map" model { file = "/net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6f36_4176/03_2025/6f36_4176.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.92, per 1000 atoms: 0.66 Number of scatterers: 7453 At special positions: 0 Unit cell: (104.975, 98.345, 130.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1279 8.00 N 1204 7.00 C 4930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" CA THR D 110 " - pdb=" N GLU D 111 " distance=2.45 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 85 " --> pdb=" O MET A 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 91 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 126 removed outlier: 4.110A pdb=" N LEU A 105 " --> pdb=" O GLY A 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 85 " --> pdb=" O MET B 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL B 120 " --> pdb=" O PHE B 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.689A pdb=" N GLY C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 85 " --> pdb=" O MET C 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG C 91 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 122 " --> pdb=" O LEU C 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.294A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 85 " --> pdb=" O MET D 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL D 120 " --> pdb=" O PHE D 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE D 122 " --> pdb=" O LEU D 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.804A pdb=" N LYS E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 85 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG E 91 " --> pdb=" O ASN E 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN E 92 " --> pdb=" O GLY E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 126 removed outlier: 4.108A pdb=" N LEU E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY F 65 " --> pdb=" O MET F 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU F 85 " --> pdb=" O MET F 81 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN F 92 " --> pdb=" O GLY F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 60 removed outlier: 3.806A pdb=" N LYS G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY G 65 " --> pdb=" O MET G 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU G 85 " --> pdb=" O MET G 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG G 91 " --> pdb=" O ASN G 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN G 92 " --> pdb=" O GLY G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL G 120 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE G 122 " --> pdb=" O LEU G 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.805A pdb=" N LYS H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY H 65 " --> pdb=" O MET H 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU H 85 " --> pdb=" O MET H 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE H 86 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 126 removed outlier: 4.108A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL H 120 " --> pdb=" O PHE H 116 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE H 122 " --> pdb=" O LEU H 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 60 removed outlier: 3.805A pdb=" N LYS I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 68 removed outlier: 3.688A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU I 85 " --> pdb=" O MET I 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN I 92 " --> pdb=" O GLY I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE I 122 " --> pdb=" O LEU I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 3.804A pdb=" N LYS J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY J 63 " --> pdb=" O SER J 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY J 65 " --> pdb=" O MET J 61 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.293A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU J 85 " --> pdb=" O MET J 81 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE J 86 " --> pdb=" O PHE J 82 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG J 91 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN J 92 " --> pdb=" O GLY J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 126 removed outlier: 4.109A pdb=" N LEU J 105 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE J 116 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL J 120 " --> pdb=" O PHE J 116 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE J 122 " --> pdb=" O LEU J 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 134 through 142 removed outlier: 3.856A pdb=" N ASP M 140 " --> pdb=" O PRO M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 155 removed outlier: 3.613A pdb=" N TRP M 151 " --> pdb=" O SER M 147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE M 155 " --> pdb=" O TRP M 151 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 164 Processing helix chain 'M' and resid 165 through 167 No H-bonds generated for 'chain 'M' and resid 165 through 167' Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 185 through 190 removed outlier: 3.609A pdb=" N TRP M 189 " --> pdb=" O GLY M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 195 removed outlier: 3.540A pdb=" N LEU M 195 " --> pdb=" O THR M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 226 removed outlier: 4.007A pdb=" N PHE M 221 " --> pdb=" O MET M 217 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL M 222 " --> pdb=" O ALA M 218 " (cutoff:3.500A) Proline residue: M 223 - end of helix Processing helix chain 'M' and resid 226 through 259 removed outlier: 4.352A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER M 235 " --> pdb=" O PHE M 231 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG M 239 " --> pdb=" O SER M 235 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET M 244 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU M 251 " --> pdb=" O GLY M 247 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS M 252 " --> pdb=" O HIS M 248 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE M 253 " --> pdb=" O THR M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 260 through 265 Processing helix chain 'M' and resid 273 through 309 removed outlier: 3.679A pdb=" N LEU M 284 " --> pdb=" O LEU M 280 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL M 285 " --> pdb=" O LEU M 281 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU M 287 " --> pdb=" O ALA M 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU M 294 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY M 297 " --> pdb=" O VAL M 293 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE M 301 " --> pdb=" O GLY M 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 78 Processing helix chain 'N' and resid 83 through 91 removed outlier: 3.515A pdb=" N ASP N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 110 removed outlier: 3.535A pdb=" N ASP N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN N 106 " --> pdb=" O ASP N 102 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 110 through 118 removed outlier: 3.635A pdb=" N SER N 117 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER N 118 " --> pdb=" O ILE N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 130 removed outlier: 4.557A pdb=" N PHE N 127 " --> pdb=" O ARG N 123 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1 1.11 - 1.29: 1143 1.29 - 1.46: 3001 1.46 - 1.64: 3371 1.64 - 1.81: 66 Bond restraints: 7582 Sorted by residual: bond pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 1.334 0.940 0.394 1.43e-02 4.89e+03 7.59e+02 bond pdb=" CB TRP M 151 " pdb=" CG TRP M 151 " ideal model delta sigma weight residual 1.498 1.417 0.081 3.10e-02 1.04e+03 6.89e+00 bond pdb=" CB ARG N 89 " pdb=" CG ARG N 89 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.05e+00 bond pdb=" CG LEU M 245 " pdb=" CD2 LEU M 245 " ideal model delta sigma weight residual 1.521 1.442 0.079 3.30e-02 9.18e+02 5.73e+00 bond pdb=" C ARG M 239 " pdb=" N LEU M 240 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.38e-02 5.25e+03 5.48e+00 ... (remaining 7577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9662 2.09 - 4.18: 491 4.18 - 6.28: 108 6.28 - 8.37: 22 8.37 - 10.46: 6 Bond angle restraints: 10289 Sorted by residual: angle pdb=" N ARG M 239 " pdb=" CA ARG M 239 " pdb=" C ARG M 239 " ideal model delta sigma weight residual 111.69 105.29 6.40 1.23e+00 6.61e-01 2.70e+01 angle pdb=" CA VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 118.40 112.73 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" N GLY M 317 " pdb=" CA GLY M 317 " pdb=" C GLY M 317 " ideal model delta sigma weight residual 112.34 121.03 -8.69 2.04e+00 2.40e-01 1.81e+01 angle pdb=" C PRO M 169 " pdb=" N PHE M 170 " pdb=" CA PHE M 170 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 angle pdb=" O VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 122.17 126.78 -4.61 1.23e+00 6.61e-01 1.41e+01 ... (remaining 10284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 4013 14.81 - 29.61: 261 29.61 - 44.42: 74 44.42 - 59.22: 3 59.22 - 74.03: 2 Dihedral angle restraints: 4353 sinusoidal: 1483 harmonic: 2870 Sorted by residual: dihedral pdb=" CA PRO M 223 " pdb=" C PRO M 223 " pdb=" N LEU M 224 " pdb=" CA LEU M 224 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE N 80 " pdb=" C PHE N 80 " pdb=" N GLY N 81 " pdb=" CA GLY N 81 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER M 187 " pdb=" C SER M 187 " pdb=" N VAL M 188 " pdb=" CA VAL M 188 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 968 0.068 - 0.137: 289 0.137 - 0.205: 17 0.205 - 0.273: 0 0.273 - 0.341: 12 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1283 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO M 262 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 222 " 0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO M 223 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO M 223 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 204 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO M 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 205 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 205 " -0.037 5.00e-02 4.00e+02 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2504 2.82 - 3.34: 7173 3.34 - 3.86: 11838 3.86 - 4.38: 15001 4.38 - 4.90: 23179 Nonbonded interactions: 59695 Sorted by model distance: nonbonded pdb=" O VAL M 238 " pdb=" CA ARG M 239 " model vdw 2.304 2.776 nonbonded pdb=" O ALA H 58 " pdb=" OG SER I 59 " model vdw 2.349 3.040 nonbonded pdb=" OD2 ASP M 140 " pdb=" NZ LYS M 144 " model vdw 2.379 3.120 nonbonded pdb=" O ASN M 121 " pdb=" NH2 ARG M 145 " model vdw 2.405 3.120 nonbonded pdb=" O SER M 142 " pdb=" OG SER M 142 " model vdw 2.439 3.040 ... (remaining 59690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 217.810 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.060 Find NCS groups from input model: 0.200 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.394 7582 Z= 0.617 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.92 (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 TRP 0.031 0.004 TRP M 189 HIS 0.020 0.003 HIS M 248 PHE 0.029 0.003 PHE M 204 TYR 0.016 0.003 TYR M 114 ARG 0.007 0.001 ARG N 130 *********************** 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 : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 84 SER cc_start: 0.7963 (m) cc_final: 0.7712 (p) REVERT: D 113 ILE cc_start: 0.6589 (mm) cc_final: 0.6287 (mm) REVERT: E 69 ILE cc_start: 0.7754 (mt) cc_final: 0.7530 (mm) REVERT: E 87 ASN cc_start: 0.5815 (t0) cc_final: 0.5352 (t0) REVERT: H 95 ILE cc_start: 0.5632 (tt) cc_final: 0.5123 (mt) REVERT: H 115 LEU cc_start: 0.5771 (mm) cc_final: 0.5513 (tt) REVERT: M 132 ASP cc_start: 0.7950 (m-30) cc_final: 0.7591 (m-30) REVERT: M 229 TYR cc_start: 0.7730 (t80) cc_final: 0.7484 (t80) outliers start: 2 outliers final: 0 residues processed: 222 average time/residue: 0.2075 time to fit residues: 63.8103 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 : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.0870 chunk 75 optimal weight: 0.0270 chunk 42 optimal weight: 0.0070 chunk 25 optimal weight: 0.3980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 78 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.0770 overall best weight: 0.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN M 243 ASN M 252 HIS N 93 GLN N 109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.140556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.4070 r_free = 0.4070 target = 0.126679 restraints weight = 20064.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.126301 restraints weight = 23506.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.125500 restraints weight = 16766.517| |-----------------------------------------------------------------------------| r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7582 Z= 0.190 Angle : 0.702 9.548 10289 Z= 0.349 Chirality : 0.041 0.275 1286 Planarity : 0.005 0.047 1259 Dihedral : 6.053 45.544 1064 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.34 % Rotamer: Outliers : 4.12 % Allowed : 17.15 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.22), residues: 1015 helix: -2.64 (0.14), residues: 811 sheet: None (None), residues: 0 loop : -1.84 (0.45), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 117 HIS 0.002 0.001 HIS M 252 PHE 0.034 0.002 PHE E 116 TYR 0.015 0.001 TYR N 88 ARG 0.005 0.000 ARG M 239 *********************** 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 175 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7381 (mm) cc_final: 0.7010 (mt) REVERT: D 116 PHE cc_start: 0.5839 (OUTLIER) cc_final: 0.5000 (t80) REVERT: E 87 ASN cc_start: 0.5213 (t0) cc_final: 0.4879 (t0) REVERT: F 61 MET cc_start: 0.7190 (mmm) cc_final: 0.6691 (mpp) REVERT: G 68 THR cc_start: 0.6904 (p) cc_final: 0.6632 (t) REVERT: J 111 GLU cc_start: 0.4467 (OUTLIER) cc_final: 0.3715 (tt0) REVERT: M 132 ASP cc_start: 0.7677 (m-30) cc_final: 0.7335 (m-30) REVERT: M 164 LEU cc_start: 0.8063 (mt) cc_final: 0.7822 (mt) REVERT: M 171 ASN cc_start: 0.8098 (t0) cc_final: 0.7777 (t0) REVERT: M 294 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7458 (tt) outliers start: 31 outliers final: 16 residues processed: 163 average time/residue: 0.1637 time to fit residues: 38.3774 Evaluate side-chains 123 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D 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 110 THR Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain J residue 59 SER Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 284 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 90 optimal weight: 0.1980 chunk 88 optimal weight: 0.0570 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 0.0010 chunk 23 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 overall best weight: 0.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 109 GLN ** 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 = 0.4184 r_free = 0.4184 target = 0.135868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3983 r_free = 0.3983 target = 0.120991 restraints weight = 20228.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.120224 restraints weight = 21227.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.121114 restraints weight = 15755.790| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 7582 Z= 0.213 Angle : 0.649 8.005 10289 Z= 0.326 Chirality : 0.043 0.375 1286 Planarity : 0.004 0.043 1259 Dihedral : 5.574 47.467 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.95 % Rotamer: Outliers : 5.05 % Allowed : 19.95 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.26), residues: 1015 helix: -1.45 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -0.83 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 117 HIS 0.004 0.001 HIS M 248 PHE 0.034 0.002 PHE D 107 TYR 0.011 0.001 TYR J 102 ARG 0.002 0.000 ARG I 91 *********************** 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 158 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7281 (mm) cc_final: 0.7016 (mt) REVERT: F 61 MET cc_start: 0.7579 (mmm) cc_final: 0.7294 (mpp) REVERT: G 116 PHE cc_start: 0.5648 (OUTLIER) cc_final: 0.5069 (m-80) REVERT: I 61 MET cc_start: 0.4395 (mmt) cc_final: 0.3871 (tpp) REVERT: I 78 LEU cc_start: 0.6222 (pp) cc_final: 0.5215 (tt) REVERT: I 91 ARG cc_start: 0.6013 (mmm160) cc_final: 0.5693 (mmm160) REVERT: J 111 GLU cc_start: 0.5079 (OUTLIER) cc_final: 0.4485 (tt0) REVERT: J 116 PHE cc_start: 0.6238 (t80) cc_final: 0.5993 (t80) REVERT: M 171 ASN cc_start: 0.8213 (t0) cc_final: 0.7987 (t0) REVERT: M 294 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7567 (tt) outliers start: 38 outliers final: 21 residues processed: 145 average time/residue: 0.1648 time to fit residues: 33.9897 Evaluate side-chains 119 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 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 294 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 90 optimal weight: 0.0670 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 70 optimal weight: 0.1980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.0970 overall best weight: 0.1514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 92 ASN ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4197 r_free = 0.4197 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 134)---------------| | r_work = 0.3991 r_free = 0.3991 target = 0.121582 restraints weight = 20029.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.120811 restraints weight = 20243.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.121502 restraints weight = 16442.088| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 7582 Z= 0.180 Angle : 0.609 8.398 10289 Z= 0.301 Chirality : 0.040 0.221 1286 Planarity : 0.004 0.037 1259 Dihedral : 5.284 47.547 1064 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.56 % Favored : 97.34 % Rotamer: Outliers : 5.32 % Allowed : 20.35 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.27), residues: 1015 helix: -0.86 (0.18), residues: 808 sheet: None (None), residues: 0 loop : -0.60 (0.51), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 117 HIS 0.002 0.001 HIS M 248 PHE 0.028 0.001 PHE D 107 TYR 0.011 0.001 TYR N 88 ARG 0.001 0.000 ARG M 239 *********************** 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 149 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7683 (mm) cc_final: 0.7438 (mt) REVERT: C 81 MET cc_start: 0.7088 (tmt) cc_final: 0.6605 (tmt) REVERT: D 113 ILE cc_start: 0.6628 (mm) cc_final: 0.6358 (mt) REVERT: E 105 LEU cc_start: 0.3913 (tt) cc_final: 0.1743 (mt) REVERT: F 61 MET cc_start: 0.7688 (mmm) cc_final: 0.7486 (mpp) REVERT: G 116 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5238 (m-80) REVERT: I 71 LEU cc_start: 0.6989 (tt) cc_final: 0.6736 (mt) REVERT: I 91 ARG cc_start: 0.5942 (mmm160) cc_final: 0.5569 (mmm160) REVERT: M 171 ASN cc_start: 0.8044 (t0) cc_final: 0.7774 (t0) REVERT: M 294 LEU cc_start: 0.8126 (tt) cc_final: 0.7604 (tt) outliers start: 40 outliers final: 22 residues processed: 141 average time/residue: 0.1580 time to fit residues: 31.6948 Evaluate side-chains 118 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 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: chunk 19 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 73 optimal weight: 0.0470 chunk 71 optimal weight: 0.0470 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4143 r_free = 0.4143 target = 0.132624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3933 r_free = 0.3933 target = 0.117439 restraints weight = 19745.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.115210 restraints weight = 19830.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.115897 restraints weight = 14746.915| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7582 Z= 0.234 Angle : 0.654 9.603 10289 Z= 0.322 Chirality : 0.041 0.238 1286 Planarity : 0.004 0.041 1259 Dihedral : 5.380 48.086 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 6.38 % Allowed : 20.08 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.27), residues: 1015 helix: -0.51 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -0.70 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 85 HIS 0.005 0.001 HIS M 248 PHE 0.021 0.002 PHE F 116 TYR 0.010 0.001 TYR I 102 ARG 0.001 0.000 ARG M 232 *********************** 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 160 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 112 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 81 MET cc_start: 0.7399 (tmt) cc_final: 0.6951 (tmt) REVERT: D 81 MET cc_start: 0.7696 (ttp) cc_final: 0.6934 (tmm) REVERT: D 118 LEU cc_start: 0.5357 (pp) cc_final: 0.5118 (pp) REVERT: E 71 LEU cc_start: 0.7938 (mm) cc_final: 0.7570 (mt) REVERT: E 78 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5832 (tp) REVERT: E 105 LEU cc_start: 0.4378 (tt) cc_final: 0.3981 (tp) REVERT: F 61 MET cc_start: 0.7641 (mmm) cc_final: 0.7064 (mpp) REVERT: G 81 MET cc_start: 0.7176 (tpt) cc_final: 0.6586 (tmm) REVERT: G 116 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: I 91 ARG cc_start: 0.5999 (mmm160) cc_final: 0.5589 (mmm160) REVERT: M 229 TYR cc_start: 0.8153 (t80) cc_final: 0.7765 (t80) REVERT: M 294 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7608 (tt) outliers start: 48 outliers final: 28 residues processed: 148 average time/residue: 0.1540 time to fit residues: 32.8209 Evaluate side-chains 132 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 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 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 80 PHE Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 91 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 70 optimal weight: 0.0010 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 44 optimal weight: 0.4980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4115 r_free = 0.4115 target = 0.130563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3853 r_free = 0.3853 target = 0.113412 restraints weight = 20017.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.114003 restraints weight = 15853.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.114401 restraints weight = 12714.535| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7582 Z= 0.248 Angle : 0.680 10.911 10289 Z= 0.331 Chirality : 0.042 0.239 1286 Planarity : 0.004 0.047 1259 Dihedral : 5.431 46.791 1064 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 6.78 % Allowed : 21.14 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.27), residues: 1015 helix: -0.31 (0.18), residues: 806 sheet: None (None), residues: 0 loop : -1.02 (0.47), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 215 HIS 0.005 0.001 HIS M 248 PHE 0.023 0.002 PHE A 116 TYR 0.010 0.001 TYR D 102 ARG 0.001 0.000 ARG M 239 *********************** 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 158 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 107 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: B 95 ILE cc_start: 0.4822 (tt) cc_final: 0.4287 (mt) REVERT: D 81 MET cc_start: 0.7214 (ttp) cc_final: 0.6911 (tmm) REVERT: E 105 LEU cc_start: 0.4505 (OUTLIER) cc_final: 0.4242 (tp) REVERT: E 111 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6176 (mt-10) REVERT: F 61 MET cc_start: 0.7471 (mmm) cc_final: 0.6674 (mpp) REVERT: G 116 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: I 71 LEU cc_start: 0.7101 (tt) cc_final: 0.6829 (mt) REVERT: I 91 ARG cc_start: 0.5807 (mmm160) cc_final: 0.5430 (mmm160) REVERT: M 294 LEU cc_start: 0.8187 (tt) cc_final: 0.7876 (tt) outliers start: 51 outliers final: 40 residues processed: 147 average time/residue: 0.1518 time to fit residues: 32.2210 Evaluate side-chains 139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 97 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 D residue 80 VAL Chi-restraints excluded: chain D residue 113 ILE 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 55 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 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 125 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 74 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 238 VAL Chi-restraints excluded: chain M residue 249 THR 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 86 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 0.0470 chunk 41 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.1980 chunk 53 optimal weight: 0.2980 chunk 59 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4116 r_free = 0.4116 target = 0.130555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.115620 restraints weight = 19829.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114603 restraints weight = 20107.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.113538 restraints weight = 19941.894| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 7582 Z= 0.234 Angle : 0.665 9.846 10289 Z= 0.324 Chirality : 0.042 0.235 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.364 46.536 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 6.38 % Allowed : 22.61 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.27), residues: 1015 helix: -0.17 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.90 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 PHE 0.032 0.002 PHE F 116 TYR 0.009 0.001 TYR N 88 ARG 0.001 0.000 ARG M 232 *********************** 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 156 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 108 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: B 95 ILE cc_start: 0.4689 (tt) cc_final: 0.4360 (mt) REVERT: D 81 MET cc_start: 0.7294 (ttp) cc_final: 0.6931 (tmm) REVERT: F 61 MET cc_start: 0.7418 (mmm) cc_final: 0.6593 (mpp) REVERT: G 107 PHE cc_start: 0.7016 (t80) cc_final: 0.6564 (t80) REVERT: G 116 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: H 61 MET cc_start: 0.6605 (mmm) cc_final: 0.5976 (mmm) REVERT: I 71 LEU cc_start: 0.7129 (tt) cc_final: 0.6834 (mt) REVERT: I 82 PHE cc_start: 0.6201 (m-10) cc_final: 0.5933 (m-10) REVERT: I 91 ARG cc_start: 0.5838 (mmm160) cc_final: 0.5418 (mmm160) REVERT: J 82 PHE cc_start: 0.7958 (m-80) cc_final: 0.7452 (t80) REVERT: M 294 LEU cc_start: 0.8191 (tt) cc_final: 0.7887 (tt) outliers start: 48 outliers final: 40 residues processed: 146 average time/residue: 0.1454 time to fit residues: 30.6111 Evaluate side-chains 142 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 101 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 D residue 80 VAL Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 81 MET 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 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 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: chunk 12 optimal weight: 0.5980 chunk 71 optimal weight: 0.3980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 11 optimal weight: 0.1980 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 51 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 0.0170 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4148 r_free = 0.4148 target = 0.132914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 150)---------------| | r_work = 0.3913 r_free = 0.3913 target = 0.116749 restraints weight = 19826.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.116876 restraints weight = 14755.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.117254 restraints weight = 11640.241| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 7582 Z= 0.186 Angle : 0.648 11.982 10289 Z= 0.310 Chirality : 0.040 0.234 1286 Planarity : 0.003 0.046 1259 Dihedral : 5.171 47.021 1064 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 5.72 % Allowed : 23.14 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.27), residues: 1015 helix: 0.05 (0.19), residues: 809 sheet: None (None), residues: 0 loop : -0.73 (0.48), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 215 HIS 0.002 0.001 HIS M 248 PHE 0.029 0.001 PHE F 116 TYR 0.011 0.001 TYR N 88 ARG 0.001 0.000 ARG M 239 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 106 time to evaluate : 0.790 Fit side-chains REVERT: C 81 MET cc_start: 0.7288 (tmt) cc_final: 0.6927 (tmt) REVERT: D 81 MET cc_start: 0.7158 (ttp) cc_final: 0.6932 (tmm) REVERT: E 97 LYS cc_start: 0.4888 (mmtm) cc_final: 0.4458 (tppt) REVERT: F 60 LYS cc_start: 0.6602 (mmtt) cc_final: 0.5831 (ttmt) REVERT: F 61 MET cc_start: 0.7455 (mmm) cc_final: 0.6559 (mpp) REVERT: G 81 MET cc_start: 0.7017 (tpt) cc_final: 0.6742 (tmm) REVERT: G 116 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5447 (m-80) REVERT: H 61 MET cc_start: 0.6891 (mmm) cc_final: 0.6217 (mmm) REVERT: H 116 PHE cc_start: 0.6058 (OUTLIER) cc_final: 0.5582 (m-80) REVERT: I 71 LEU cc_start: 0.7152 (tt) cc_final: 0.6867 (mt) REVERT: I 91 ARG cc_start: 0.6014 (mmm160) cc_final: 0.5494 (mmm160) REVERT: J 82 PHE cc_start: 0.7771 (m-80) cc_final: 0.7389 (t80) REVERT: M 294 LEU cc_start: 0.8115 (tt) cc_final: 0.7813 (tt) outliers start: 43 outliers final: 35 residues processed: 142 average time/residue: 0.1476 time to fit residues: 30.4864 Evaluate side-chains 137 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 62 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 81 MET 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 265 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 79 LEU Chi-restraints excluded: chain N residue 84 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 52 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4126 r_free = 0.4126 target = 0.131283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 152)---------------| | r_work = 0.3880 r_free = 0.3880 target = 0.114928 restraints weight = 20233.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.115023 restraints weight = 16332.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115573 restraints weight = 12848.009| |-----------------------------------------------------------------------------| r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7582 Z= 0.225 Angle : 0.662 8.562 10289 Z= 0.320 Chirality : 0.042 0.238 1286 Planarity : 0.003 0.047 1259 Dihedral : 5.270 46.662 1064 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 5.59 % Allowed : 23.80 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.28), residues: 1015 helix: 0.09 (0.19), residues: 806 sheet: None (None), residues: 0 loop : -0.69 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 PHE 0.027 0.002 PHE F 116 TYR 0.010 0.001 TYR D 102 ARG 0.001 0.000 ARG M 145 *********************** 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 146 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7171 (tmt) cc_final: 0.6857 (tmt) REVERT: D 81 MET cc_start: 0.7176 (ttp) cc_final: 0.6939 (tmm) REVERT: E 97 LYS cc_start: 0.4663 (mmtm) cc_final: 0.4204 (tppt) REVERT: F 60 LYS cc_start: 0.6612 (mmtt) cc_final: 0.5938 (ttmt) REVERT: F 61 MET cc_start: 0.7323 (mmm) cc_final: 0.6722 (mpp) REVERT: G 116 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: H 61 MET cc_start: 0.6834 (mmm) cc_final: 0.6273 (mmm) REVERT: H 116 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5604 (m-80) REVERT: I 71 LEU cc_start: 0.7216 (tt) cc_final: 0.6955 (mt) REVERT: I 91 ARG cc_start: 0.5983 (mmm160) cc_final: 0.5710 (mmm160) REVERT: J 82 PHE cc_start: 0.7859 (m-80) cc_final: 0.7416 (t80) REVERT: M 294 LEU cc_start: 0.8137 (tt) cc_final: 0.7865 (tt) outliers start: 42 outliers final: 36 residues processed: 139 average time/residue: 0.1508 time to fit residues: 30.6882 Evaluate side-chains 138 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 94 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 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 81 MET 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 265 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 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 74 optimal weight: 0.0060 chunk 85 optimal weight: 0.3980 chunk 5 optimal weight: 0.5980 chunk 99 optimal weight: 0.2980 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4136 r_free = 0.4136 target = 0.131991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 143)---------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115702 restraints weight = 20198.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.116057 restraints weight = 14442.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.116403 restraints weight = 11995.375| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.6343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7582 Z= 0.204 Angle : 0.656 12.133 10289 Z= 0.314 Chirality : 0.042 0.296 1286 Planarity : 0.003 0.047 1259 Dihedral : 5.178 46.544 1064 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 5.32 % Allowed : 24.20 % Favored : 70.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 1015 helix: 0.20 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.67 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 PHE 0.026 0.001 PHE F 116 TYR 0.011 0.001 TYR D 102 ARG 0.001 0.000 ARG M 145 ********************** 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: 40 poor density : 105 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7235 (tmt) cc_final: 0.6922 (tmt) REVERT: D 81 MET cc_start: 0.7320 (ttp) cc_final: 0.6987 (tmm) REVERT: E 97 LYS cc_start: 0.4485 (mmtm) cc_final: 0.4015 (tppt) REVERT: F 60 LYS cc_start: 0.6429 (mmtt) cc_final: 0.6112 (ttmm) REVERT: F 61 MET cc_start: 0.7299 (mmm) cc_final: 0.6817 (mpp) REVERT: H 61 MET cc_start: 0.6781 (mmm) cc_final: 0.6244 (mmm) REVERT: H 116 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: I 71 LEU cc_start: 0.7202 (tt) cc_final: 0.6952 (mt) REVERT: I 91 ARG cc_start: 0.5984 (mmm160) cc_final: 0.5441 (mmm160) REVERT: J 56 LEU cc_start: 0.6740 (mt) cc_final: 0.6031 (tp) REVERT: J 82 PHE cc_start: 0.7804 (m-80) cc_final: 0.7444 (t80) REVERT: M 294 LEU cc_start: 0.8120 (tt) cc_final: 0.7823 (tt) outliers start: 40 outliers final: 35 residues processed: 140 average time/residue: 0.1474 time to fit residues: 29.9693 Evaluate side-chains 136 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET 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 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU 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 265 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 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 0.3980 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 97 optimal weight: 0.0980 chunk 81 optimal weight: 0.4980 chunk 70 optimal weight: 0.0070 overall best weight: 0.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 GLN ** 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 = 0.4151 r_free = 0.4151 target = 0.132939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 141)---------------| | r_work = 0.3946 r_free = 0.3946 target = 0.118167 restraints weight = 19764.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.116021 restraints weight = 21129.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.116688 restraints weight = 15148.856| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7582 Z= 0.191 Angle : 0.640 8.607 10289 Z= 0.308 Chirality : 0.041 0.274 1286 Planarity : 0.003 0.047 1259 Dihedral : 5.087 46.509 1064 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 4.79 % Allowed : 24.87 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.28), residues: 1015 helix: 0.26 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -0.62 (0.48), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 112 HIS 0.003 0.001 HIS M 248 PHE 0.025 0.001 PHE F 116 TYR 0.013 0.001 TYR D 102 ARG 0.001 0.000 ARG M 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4074.93 seconds wall clock time: 72 minutes 19.10 seconds (4339.10 seconds total)