Starting phenix.real_space_refine on Tue Sep 24 07:23:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_4176.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_4176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_4176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_4176.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/09_2024/6f36_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-5461/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: 4.96, per 1000 atoms: 0.67 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: 1.72 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: 0.63 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: 1.90 Time building geometry restraints manager: 2.03 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: 6.670 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.640 Find NCS groups from input model: 0.190 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.440 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 2 poor density : 220 time to evaluate : 1.075 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: 0.1637 time to fit residues: 50.3741 Evaluate side-chains 117 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 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 fitting. rotamer outliers: 31 poor density : 144 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7435 (mm) cc_final: 0.7053 (mt) REVERT: D 116 PHE cc_start: 0.6005 (OUTLIER) cc_final: 0.5149 (t80) REVERT: E 87 ASN cc_start: 0.5305 (t0) cc_final: 0.4922 (t0) REVERT: F 61 MET cc_start: 0.7265 (mmm) cc_final: 0.6585 (mpp) REVERT: G 68 THR cc_start: 0.7048 (p) cc_final: 0.6780 (t) REVERT: J 111 GLU cc_start: 0.4512 (OUTLIER) cc_final: 0.3786 (tt0) REVERT: M 132 ASP cc_start: 0.7787 (m-30) cc_final: 0.7454 (m-30) REVERT: M 164 LEU cc_start: 0.8033 (mt) cc_final: 0.7792 (mt) REVERT: M 171 ASN cc_start: 0.8048 (t0) cc_final: 0.7715 (t0) REVERT: M 294 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7425 (tt) outliers start: 31 outliers final: 16 residues processed: 163 average time/residue: 0.1528 time to fit residues: 35.4524 Evaluate side-chains 123 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.2980 chunk 28 optimal weight: 0.5980 chunk 75 optimal weight: 0.0670 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 98 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 72 optimal weight: 0.0980 chunk 89 optimal weight: 0.1980 overall best weight: 0.1416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.4059 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= 0.186 Angle : 0.627 8.020 10289 Z= 0.313 Chirality : 0.042 0.398 1286 Planarity : 0.004 0.040 1259 Dihedral : 5.461 47.554 1064 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 4.26 % Allowed : 20.21 % Favored : 75.53 % 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: -2.14 (0.26), residues: 1015 helix: -1.42 (0.17), residues: 797 sheet: None (None), residues: 0 loop : -0.49 (0.50), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 241 HIS 0.002 0.001 HIS M 248 PHE 0.034 0.001 PHE D 107 TYR 0.011 0.001 TYR N 88 ARG 0.002 0.000 ARG J 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 152 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 0.730 Fit side-chains REVERT: B 69 ILE cc_start: 0.7342 (mm) cc_final: 0.7085 (mt) REVERT: C 81 MET cc_start: 0.6942 (tmt) cc_final: 0.6497 (tmt) REVERT: D 113 ILE cc_start: 0.6649 (mm) cc_final: 0.6261 (mm) REVERT: F 61 MET cc_start: 0.7641 (mmm) cc_final: 0.7222 (mpp) REVERT: G 99 LEU cc_start: 0.5244 (mt) cc_final: 0.4911 (mp) REVERT: G 116 PHE cc_start: 0.5690 (OUTLIER) cc_final: 0.5054 (m-80) REVERT: H 61 MET cc_start: 0.6310 (mmm) cc_final: 0.6102 (mmm) REVERT: I 61 MET cc_start: 0.4324 (mmt) cc_final: 0.3815 (tpp) REVERT: I 78 LEU cc_start: 0.6192 (pp) cc_final: 0.5222 (tt) REVERT: I 91 ARG cc_start: 0.6045 (mmm160) cc_final: 0.5702 (mmm160) REVERT: J 111 GLU cc_start: 0.5056 (OUTLIER) cc_final: 0.4680 (mt-10) REVERT: J 116 PHE cc_start: 0.6353 (t80) cc_final: 0.5982 (t80) REVERT: M 132 ASP cc_start: 0.7512 (m-30) cc_final: 0.7152 (m-30) REVERT: M 171 ASN cc_start: 0.7963 (t0) cc_final: 0.7727 (t0) REVERT: M 294 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7436 (tt) outliers start: 32 outliers final: 15 residues processed: 142 average time/residue: 0.1522 time to fit residues: 30.7461 Evaluate side-chains 114 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 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 68 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7582 Z= 0.331 Angle : 0.761 9.471 10289 Z= 0.379 Chirality : 0.047 0.228 1286 Planarity : 0.005 0.053 1259 Dihedral : 5.949 48.484 1064 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 6.91 % Allowed : 19.28 % Favored : 73.80 % 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: -1.92 (0.26), residues: 1015 helix: -1.12 (0.17), residues: 803 sheet: None (None), residues: 0 loop : -1.07 (0.50), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 85 HIS 0.006 0.002 HIS M 248 PHE 0.024 0.002 PHE N 80 TYR 0.014 0.002 TYR I 102 ARG 0.003 0.000 ARG N 130 *********************** 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 172 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 120 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: B 95 ILE cc_start: 0.4015 (tt) cc_final: 0.3753 (mp) REVERT: D 81 MET cc_start: 0.7392 (ttp) cc_final: 0.6738 (tmm) REVERT: E 78 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6055 (tp) REVERT: G 116 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.5254 (m-80) REVERT: I 71 LEU cc_start: 0.7286 (tt) cc_final: 0.6908 (mt) REVERT: J 111 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.4330 (tt0) REVERT: J 116 PHE cc_start: 0.6502 (t80) cc_final: 0.6204 (t80) REVERT: M 294 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7681 (tt) outliers start: 52 outliers final: 28 residues processed: 163 average time/residue: 0.1595 time to fit residues: 36.8245 Evaluate side-chains 137 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 105 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL 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 C residue 78 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0070 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 0.0980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5392 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= 0.245 Angle : 0.660 8.682 10289 Z= 0.327 Chirality : 0.042 0.220 1286 Planarity : 0.004 0.044 1259 Dihedral : 5.582 47.601 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 6.52 % Allowed : 20.61 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -1.40 (0.27), residues: 1015 helix: -0.70 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -1.15 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 PHE 0.024 0.002 PHE A 116 TYR 0.020 0.002 TYR I 102 ARG 0.001 0.000 ARG J 91 *********************** 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 162 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 113 time to evaluate : 0.813 Fit side-chains REVERT: B 95 ILE cc_start: 0.4807 (tt) cc_final: 0.4293 (mt) REVERT: C 113 ILE cc_start: 0.6107 (mt) cc_final: 0.5853 (mt) REVERT: D 81 MET cc_start: 0.7163 (ttp) cc_final: 0.6709 (tmm) REVERT: D 110 THR cc_start: 0.5946 (m) cc_final: 0.5653 (p) REVERT: D 113 ILE cc_start: 0.7087 (mm) cc_final: 0.6516 (mt) REVERT: E 111 GLU cc_start: 0.6466 (mm-30) cc_final: 0.6009 (mt-10) REVERT: F 61 MET cc_start: 0.7554 (mmt) cc_final: 0.6849 (mpp) REVERT: G 81 MET cc_start: 0.7468 (mmm) cc_final: 0.7263 (tpt) REVERT: G 116 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.5338 (m-80) REVERT: H 61 MET cc_start: 0.6459 (mmm) cc_final: 0.6061 (mmm) REVERT: H 82 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4843 (m-10) REVERT: H 116 PHE cc_start: 0.5713 (OUTLIER) cc_final: 0.5216 (m-80) REVERT: I 91 ARG cc_start: 0.6027 (mmm160) cc_final: 0.5545 (mmp-170) REVERT: J 111 GLU cc_start: 0.5406 (OUTLIER) cc_final: 0.4612 (tt0) REVERT: M 294 LEU cc_start: 0.8126 (tt) cc_final: 0.7823 (tt) outliers start: 49 outliers final: 31 residues processed: 151 average time/residue: 0.1511 time to fit residues: 33.6075 Evaluate side-chains 134 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 99 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 95 ILE Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 93 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 overall best weight: 0.2580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5633 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 : 0.630 8.778 10289 Z= 0.312 Chirality : 0.040 0.213 1286 Planarity : 0.004 0.045 1259 Dihedral : 5.404 47.540 1064 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 6.52 % Allowed : 21.14 % Favored : 72.34 % 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: -0.91 (0.27), residues: 1015 helix: -0.36 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -0.95 (0.48), residues: 210 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 0.029 0.001 PHE G 107 TYR 0.014 0.001 TYR I 102 ARG 0.001 0.000 ARG J 91 *********************** 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 160 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 111 time to evaluate : 0.826 Fit side-chains REVERT: B 95 ILE cc_start: 0.4611 (tt) cc_final: 0.3970 (mt) REVERT: D 81 MET cc_start: 0.7123 (ttp) cc_final: 0.6885 (tmm) REVERT: D 110 THR cc_start: 0.5646 (m) cc_final: 0.5323 (p) REVERT: D 113 ILE cc_start: 0.6989 (mm) cc_final: 0.6707 (mt) REVERT: F 61 MET cc_start: 0.7684 (mmt) cc_final: 0.6857 (mpp) REVERT: G 116 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.5283 (m-80) REVERT: H 61 MET cc_start: 0.6035 (mmm) cc_final: 0.5603 (mmm) REVERT: H 80 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7423 (m) REVERT: H 82 PHE cc_start: 0.5326 (OUTLIER) cc_final: 0.4756 (m-10) REVERT: H 116 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: I 71 LEU cc_start: 0.7224 (tt) cc_final: 0.6938 (mt) REVERT: I 91 ARG cc_start: 0.5914 (mmm160) cc_final: 0.5206 (mmp-170) REVERT: J 111 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.4446 (tt0) REVERT: M 294 LEU cc_start: 0.8115 (tt) cc_final: 0.7819 (tt) outliers start: 49 outliers final: 35 residues processed: 150 average time/residue: 0.1455 time to fit residues: 31.6423 Evaluate side-chains 139 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain 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 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 81 MET Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 107 THR 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 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.0980 chunk 70 optimal weight: 0.0070 chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.0470 chunk 96 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.2696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5894 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= 0.211 Angle : 0.624 8.612 10289 Z= 0.308 Chirality : 0.040 0.226 1286 Planarity : 0.004 0.049 1259 Dihedral : 5.287 47.709 1064 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 6.38 % Allowed : 21.41 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (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: -0.57 (0.27), residues: 1015 helix: -0.12 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.85 (0.48), 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 0.022 0.001 PHE A 116 TYR 0.014 0.001 TYR I 102 ARG 0.001 0.000 ARG J 91 *********************** 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 152 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 104 time to evaluate : 0.802 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.6577 (mtp) cc_final: 0.6226 (ttm) REVERT: B 95 ILE cc_start: 0.4712 (tt) cc_final: 0.4399 (mt) REVERT: C 61 MET cc_start: 0.8395 (mpp) cc_final: 0.8135 (mpp) REVERT: D 81 MET cc_start: 0.7138 (ttp) cc_final: 0.6889 (tmm) REVERT: D 113 ILE cc_start: 0.6951 (mm) cc_final: 0.6667 (mt) REVERT: F 61 MET cc_start: 0.7415 (mmt) cc_final: 0.7023 (mpp) REVERT: G 116 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5528 (m-80) REVERT: H 61 MET cc_start: 0.5918 (mmm) cc_final: 0.5578 (mmm) REVERT: H 82 PHE cc_start: 0.5444 (OUTLIER) cc_final: 0.4704 (m-80) REVERT: I 71 LEU cc_start: 0.7226 (tt) cc_final: 0.6805 (mt) REVERT: I 82 PHE cc_start: 0.6433 (m-80) cc_final: 0.6202 (m-10) REVERT: I 91 ARG cc_start: 0.5957 (mmm160) cc_final: 0.5269 (mmp-170) REVERT: J 82 PHE cc_start: 0.8216 (m-80) cc_final: 0.7547 (t80) REVERT: M 294 LEU cc_start: 0.8113 (tt) cc_final: 0.7824 (tt) outliers start: 48 outliers final: 41 residues processed: 145 average time/residue: 0.1446 time to fit residues: 30.4739 Evaluate side-chains 142 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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 E residue 125 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 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 81 MET 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 107 THR Chi-restraints excluded: chain M residue 167 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 75 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 84 optimal weight: 0.0370 chunk 89 optimal weight: 0.2980 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.6075 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= 0.215 Angle : 0.626 8.697 10289 Z= 0.309 Chirality : 0.041 0.220 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.257 47.004 1064 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.05 % Favored : 96.85 % Rotamer: Outliers : 6.78 % Allowed : 21.54 % Favored : 71.68 % 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: -0.38 (0.27), residues: 1015 helix: 0.04 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.86 (0.48), 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 0.023 0.002 PHE A 116 TYR 0.014 0.001 TYR I 102 ARG 0.001 0.000 ARG E 91 *********************** 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 159 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 108 time to evaluate : 0.810 Fit side-chains REVERT: A 61 MET cc_start: 0.6508 (mtp) cc_final: 0.6301 (ttm) REVERT: D 81 MET cc_start: 0.7164 (ttp) cc_final: 0.6880 (tmm) REVERT: D 110 THR cc_start: 0.5618 (m) cc_final: 0.5402 (p) REVERT: D 113 ILE cc_start: 0.6818 (mm) cc_final: 0.6530 (mt) REVERT: E 97 LYS cc_start: 0.4964 (mmtm) cc_final: 0.4512 (tppt) REVERT: F 60 LYS cc_start: 0.6905 (mmtt) cc_final: 0.6240 (ttmt) REVERT: F 61 MET cc_start: 0.7435 (mmt) cc_final: 0.7085 (mpp) REVERT: F 107 PHE cc_start: 0.6768 (t80) cc_final: 0.6492 (t80) REVERT: G 116 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5440 (m-80) REVERT: H 61 MET cc_start: 0.6015 (mmm) cc_final: 0.5704 (mmm) REVERT: H 82 PHE cc_start: 0.5321 (OUTLIER) cc_final: 0.4438 (m-80) REVERT: H 116 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.5783 (m-80) REVERT: I 71 LEU cc_start: 0.7282 (tt) cc_final: 0.6993 (mt) REVERT: I 91 ARG cc_start: 0.5958 (mmm160) cc_final: 0.5225 (mmp-170) REVERT: J 82 PHE cc_start: 0.8105 (m-80) cc_final: 0.7501 (t80) REVERT: M 294 LEU cc_start: 0.8082 (tt) cc_final: 0.7807 (tt) outliers start: 51 outliers final: 44 residues processed: 150 average time/residue: 0.1556 time to fit residues: 33.8554 Evaluate side-chains 147 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 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 E residue 125 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 104 LEU Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 81 MET 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 107 THR Chi-restraints excluded: chain M residue 167 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 290 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 70 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 89 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 0.2354 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.6227 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= 0.198 Angle : 0.616 8.739 10289 Z= 0.304 Chirality : 0.041 0.225 1286 Planarity : 0.003 0.048 1259 Dihedral : 5.172 46.749 1064 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.35 % Favored : 96.55 % Rotamer: Outliers : 6.52 % Allowed : 21.81 % Favored : 71.68 % 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: -0.15 (0.28), residues: 1015 helix: 0.18 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.68 (0.48), residues: 211 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 0.033 0.002 PHE G 107 TYR 0.013 0.001 TYR I 102 ARG 0.004 0.000 ARG M 133 *********************** 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 155 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 106 time to evaluate : 0.737 Fit side-chains REVERT: A 61 MET cc_start: 0.6918 (mtp) cc_final: 0.6705 (ttm) REVERT: C 81 MET cc_start: 0.7076 (tmt) cc_final: 0.6753 (tmt) REVERT: D 81 MET cc_start: 0.7231 (ttp) cc_final: 0.6931 (tmm) REVERT: D 110 THR cc_start: 0.5584 (m) cc_final: 0.5360 (p) REVERT: D 113 ILE cc_start: 0.6605 (mm) cc_final: 0.6346 (mt) REVERT: E 97 LYS cc_start: 0.4625 (mmtm) cc_final: 0.4151 (tppt) REVERT: F 60 LYS cc_start: 0.6999 (mmtt) cc_final: 0.6278 (ttmt) REVERT: F 61 MET cc_start: 0.7433 (mmt) cc_final: 0.7156 (mpp) REVERT: H 82 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: H 116 PHE cc_start: 0.6248 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: I 71 LEU cc_start: 0.7311 (tt) cc_final: 0.7041 (mt) REVERT: I 91 ARG cc_start: 0.5948 (mmm160) cc_final: 0.5279 (mmp-170) REVERT: J 82 PHE cc_start: 0.8111 (m-80) cc_final: 0.7558 (t80) REVERT: M 294 LEU cc_start: 0.8073 (tt) cc_final: 0.7805 (tt) REVERT: M 316 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7136 (pt) outliers start: 49 outliers final: 41 residues processed: 147 average time/residue: 0.1459 time to fit residues: 31.2630 Evaluate side-chains 141 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 97 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 E residue 125 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain I residue 81 MET 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 107 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 274 THR Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 91 optimal weight: 0.2980 chunk 79 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.6391 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= 0.271 Angle : 0.692 9.553 10289 Z= 0.341 Chirality : 0.044 0.229 1286 Planarity : 0.004 0.048 1259 Dihedral : 5.425 46.236 1064 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 6.38 % Allowed : 22.87 % Favored : 70.74 % 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: -0.40 (0.27), residues: 1015 helix: 0.02 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.86 (0.47), residues: 210 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 0.045 0.002 PHE F 107 TYR 0.015 0.002 TYR D 102 ARG 0.002 0.000 ARG M 239 ********************** 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 150 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 102 time to evaluate : 0.760 Fit side-chains REVERT: D 81 MET cc_start: 0.7367 (ttp) cc_final: 0.6991 (tmm) REVERT: D 110 THR cc_start: 0.5776 (m) cc_final: 0.5519 (p) REVERT: D 113 ILE cc_start: 0.6735 (mm) cc_final: 0.6532 (mt) REVERT: E 97 LYS cc_start: 0.4712 (mmtm) cc_final: 0.4336 (tppt) REVERT: F 60 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6395 (ttmt) REVERT: F 61 MET cc_start: 0.7566 (mmt) cc_final: 0.7214 (mpp) REVERT: H 82 PHE cc_start: 0.5619 (OUTLIER) cc_final: 0.4878 (m-80) REVERT: H 116 PHE cc_start: 0.6156 (OUTLIER) cc_final: 0.5717 (m-80) REVERT: I 71 LEU cc_start: 0.7295 (tt) cc_final: 0.6972 (mt) REVERT: I 91 ARG cc_start: 0.6073 (mmm160) cc_final: 0.5399 (mmp-170) REVERT: M 294 LEU cc_start: 0.8142 (tt) cc_final: 0.7843 (tt) REVERT: M 316 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7293 (pt) outliers start: 48 outliers final: 41 residues processed: 143 average time/residue: 0.1473 time to fit residues: 30.3219 Evaluate side-chains 140 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 61 MET 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 E residue 125 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 PHE Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 107 THR 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 290 LEU Chi-restraints excluded: chain M residue 316 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 88 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0770 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 79 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 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 = 0.4125 r_free = 0.4125 target = 0.131500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3946 r_free = 0.3946 target = 0.118462 restraints weight = 19743.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.117636 restraints weight = 21160.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.116905 restraints weight = 17726.139| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.6494 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= 0.186 Angle : 0.633 8.757 10289 Z= 0.309 Chirality : 0.041 0.226 1286 Planarity : 0.003 0.046 1259 Dihedral : 5.172 46.689 1064 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.86 % Favored : 97.04 % Rotamer: Outliers : 5.45 % Allowed : 23.80 % Favored : 70.74 % 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: -0.09 (0.28), residues: 1015 helix: 0.25 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.79 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 112 HIS 0.002 0.001 HIS M 248 PHE 0.038 0.002 PHE F 107 TYR 0.013 0.001 TYR I 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: 1999.55 seconds wall clock time: 36 minutes 19.02 seconds (2179.02 seconds total)