Starting phenix.real_space_refine on Mon Mar 11 06:44:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/03_2024/6f36_4176.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/03_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_4176/03_2024/6f36_4176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/03_2024/6f36_4176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/03_2024/6f36_4176.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6f36_4176/03_2024/6f36_4176.pdb" } 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 Residue "A ARG 91": "NH1" <-> "NH2" Residue "B ARG 91": "NH1" <-> "NH2" Residue "C ARG 91": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "M ARG 115": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "M ARG 145": "NH1" <-> "NH2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 239": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 123": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7453 Number of models: 1 Model: "" Number of chains: 12 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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} Time building chain proxies: 4.25, per 1000 atoms: 0.57 Number of scatterers: 7453 At special positions: 0 Unit cell: (104.975, 98.345, 130.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1279 8.00 N 1204 7.00 C 4930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.59 Conformation dependent library (CDL) restraints added in 1.3 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: 0.71 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: 1.83 Time building geometry restraints manager: 2.85 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: 98.17 - 105.42: 125 105.42 - 112.66: 3928 112.66 - 119.91: 2837 119.91 - 127.16: 3352 127.16 - 134.40: 47 Bond angle restraints: 10289 Sorted by residual: angle pdb=" N ARG M 239 " pdb=" CA ARG M 239 " pdb=" C ARG M 239 " ideal model delta sigma weight residual 111.69 105.29 6.40 1.23e+00 6.61e-01 2.70e+01 angle pdb=" CA VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 118.40 112.73 5.67 1.15e+00 7.56e-01 2.43e+01 angle pdb=" N GLY M 317 " pdb=" CA GLY M 317 " pdb=" C GLY M 317 " ideal model delta sigma weight residual 112.34 121.03 -8.69 2.04e+00 2.40e-01 1.81e+01 angle pdb=" C PRO M 169 " pdb=" N PHE M 170 " pdb=" CA PHE M 170 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.66e+01 angle pdb=" O VAL M 238 " pdb=" C VAL M 238 " pdb=" N ARG M 239 " ideal model delta sigma weight residual 122.17 126.78 -4.61 1.23e+00 6.61e-01 1.41e+01 ... (remaining 10284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.81: 4012 14.81 - 29.61: 259 29.61 - 44.42: 74 44.42 - 59.22: 3 59.22 - 74.03: 2 Dihedral angle restraints: 4350 sinusoidal: 1480 harmonic: 2870 Sorted by residual: dihedral pdb=" CA PRO M 223 " pdb=" C PRO M 223 " pdb=" N LEU M 224 " pdb=" CA LEU M 224 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA PHE N 80 " pdb=" C PHE N 80 " pdb=" N GLY N 81 " pdb=" CA GLY N 81 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA SER M 187 " pdb=" C SER M 187 " pdb=" N VAL M 188 " pdb=" CA VAL M 188 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 4347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 968 0.068 - 0.137: 289 0.137 - 0.205: 17 0.205 - 0.273: 0 0.273 - 0.341: 12 Chirality restraints: 1286 Sorted by residual: chirality pdb=" CB ILE C 95 " pdb=" CA ILE C 95 " pdb=" CG1 ILE C 95 " pdb=" CG2 ILE C 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB ILE D 95 " pdb=" CA ILE D 95 " pdb=" CG1 ILE D 95 " pdb=" CG2 ILE D 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE E 95 " pdb=" CA ILE E 95 " pdb=" CG1 ILE E 95 " pdb=" CG2 ILE E 95 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 1283 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.052 5.00e-02 4.00e+02 7.73e-02 9.56e+00 pdb=" N PRO M 262 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL M 222 " 0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO M 223 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO M 223 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO M 223 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE M 204 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO M 205 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 205 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 205 " -0.037 5.00e-02 4.00e+02 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2505 2.82 - 3.34: 7174 3.34 - 3.86: 11840 3.86 - 4.38: 15001 4.38 - 4.90: 23179 Nonbonded interactions: 59699 Sorted by model distance: nonbonded pdb=" O VAL M 238 " pdb=" CA ARG M 239 " model vdw 2.304 2.776 nonbonded pdb=" O ALA H 58 " pdb=" OG SER I 59 " model vdw 2.349 2.440 nonbonded pdb=" OD2 ASP M 140 " pdb=" NZ LYS M 144 " model vdw 2.379 2.520 nonbonded pdb=" O ASN M 121 " pdb=" NH2 ARG M 145 " model vdw 2.405 2.520 nonbonded pdb=" O SER M 142 " pdb=" OG SER M 142 " model vdw 2.439 2.440 ... (remaining 59694 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 4.840 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: 0.000 Extract box with map and model: 19.300 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 21.880 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.250 ------------------------------------------------------------------------------- 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= 0.655 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 : 0.870 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: 0.1595 time to fit residues: 49.0887 Evaluate side-chains 117 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.841 ------------------------------------------------------------------------------- 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: 0.0770 chunk 75 optimal weight: 0.0980 chunk 42 optimal weight: 0.0040 chunk 25 optimal weight: 0.0980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.0980 chunk 78 optimal weight: 0.0980 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 90 optimal weight: 0.0980 overall best weight: 0.0750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN G 98 GLN H 94 ASN M 243 ASN N 93 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7582 Z= 0.175 Angle : 0.694 9.686 10289 Z= 0.342 Chirality : 0.040 0.199 1286 Planarity : 0.005 0.051 1259 Dihedral : 6.008 20.031 1064 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.26 % Allowed : 17.82 % Favored : 77.93 % 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: -4.22 (0.21), residues: 1015 helix: -2.68 (0.14), residues: 811 sheet: None (None), residues: 0 loop : -2.11 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 117 HIS 0.004 0.001 HIS M 248 PHE 0.032 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 166 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7445 (mm) cc_final: 0.7098 (mt) REVERT: C 84 SER cc_start: 0.8213 (m) cc_final: 0.7990 (t) REVERT: D 109 LEU cc_start: 0.5851 (mt) cc_final: 0.5649 (mt) REVERT: E 87 ASN cc_start: 0.5238 (t0) cc_final: 0.4860 (t0) REVERT: F 61 MET cc_start: 0.7261 (mmm) cc_final: 0.6574 (mpp) REVERT: G 68 THR cc_start: 0.7062 (p) cc_final: 0.6801 (t) REVERT: J 102 TYR cc_start: 0.7107 (m-80) cc_final: 0.6868 (m-80) REVERT: M 132 ASP cc_start: 0.7809 (m-30) cc_final: 0.7465 (m-30) REVERT: M 294 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7422 (tt) outliers start: 32 outliers final: 18 residues processed: 154 average time/residue: 0.1542 time to fit residues: 33.8605 Evaluate side-chains 121 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain G residue 98 GLN 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 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: 0.0970 chunk 28 optimal weight: 0.0980 chunk 75 optimal weight: 0.0070 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.0670 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 89 optimal weight: 0.8980 overall best weight: 0.0632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 ASN M 252 HIS ** 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: 0.6995 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7582 Z= 0.151 Angle : 0.590 8.898 10289 Z= 0.290 Chirality : 0.040 0.432 1286 Planarity : 0.004 0.042 1259 Dihedral : 5.322 16.786 1064 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.99 % Allowed : 19.95 % Favored : 76.06 % 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: -2.34 (0.25), residues: 1015 helix: -1.53 (0.16), residues: 795 sheet: None (None), residues: 0 loop : -0.72 (0.49), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 241 HIS 0.002 0.000 HIS M 248 PHE 0.029 0.001 PHE D 107 TYR 0.011 0.001 TYR N 88 ARG 0.002 0.000 ARG M 239 *********************** 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: 30 poor density : 122 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7389 (mm) cc_final: 0.7136 (mt) REVERT: B 81 MET cc_start: 0.7161 (tmm) cc_final: 0.6931 (tmm) REVERT: C 81 MET cc_start: 0.6904 (tmt) cc_final: 0.6510 (tmt) REVERT: C 84 SER cc_start: 0.8378 (m) cc_final: 0.8163 (t) REVERT: F 61 MET cc_start: 0.7566 (mmm) cc_final: 0.7162 (mpp) REVERT: G 116 PHE cc_start: 0.5515 (OUTLIER) cc_final: 0.4822 (m-80) REVERT: I 78 LEU cc_start: 0.6183 (pp) cc_final: 0.5241 (tt) REVERT: I 91 ARG cc_start: 0.5998 (mmm160) cc_final: 0.5552 (mmm160) REVERT: J 82 PHE cc_start: 0.7767 (OUTLIER) cc_final: 0.7307 (t80) REVERT: J 102 TYR cc_start: 0.6945 (m-80) cc_final: 0.6727 (m-80) REVERT: J 116 PHE cc_start: 0.6351 (t80) cc_final: 0.6044 (t80) REVERT: M 132 ASP cc_start: 0.7599 (m-30) cc_final: 0.7308 (m-30) REVERT: M 171 ASN cc_start: 0.8127 (t0) cc_final: 0.7835 (t0) REVERT: M 271 VAL cc_start: 0.7147 (OUTLIER) cc_final: 0.6800 (p) REVERT: M 294 LEU cc_start: 0.7901 (tt) cc_final: 0.7489 (tt) outliers start: 30 outliers final: 11 residues processed: 145 average time/residue: 0.1557 time to fit residues: 32.3775 Evaluate side-chains 119 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 92 ASN 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 82 PHE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain 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: 0.5980 chunk 10 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 0.1980 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.0000 chunk 54 optimal weight: 0.4980 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 87 ASN E 92 ASN ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** N 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7582 Z= 0.196 Angle : 0.605 6.618 10289 Z= 0.298 Chirality : 0.041 0.291 1286 Planarity : 0.004 0.041 1259 Dihedral : 5.189 17.239 1064 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.52 % Allowed : 21.94 % Favored : 73.54 % 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: -1.54 (0.26), residues: 1015 helix: -0.86 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -0.88 (0.50), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 117 HIS 0.003 0.001 HIS M 248 PHE 0.022 0.002 PHE F 116 TYR 0.008 0.001 TYR D 102 ARG 0.001 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 144 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 110 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 69 ILE cc_start: 0.7576 (mm) cc_final: 0.7328 (mt) REVERT: C 81 MET cc_start: 0.7186 (tmt) cc_final: 0.6693 (tmt) REVERT: C 84 SER cc_start: 0.8438 (m) cc_final: 0.8212 (t) REVERT: D 110 THR cc_start: 0.6316 (m) cc_final: 0.6079 (p) REVERT: E 78 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.6009 (tp) REVERT: F 61 MET cc_start: 0.7794 (mmm) cc_final: 0.7365 (mpp) REVERT: F 82 PHE cc_start: 0.5615 (m-10) cc_final: 0.5336 (m-10) REVERT: G 81 MET cc_start: 0.6925 (tpt) cc_final: 0.6510 (tmm) REVERT: G 99 LEU cc_start: 0.5428 (mt) cc_final: 0.5226 (mp) REVERT: G 116 PHE cc_start: 0.5980 (OUTLIER) cc_final: 0.5441 (m-80) REVERT: I 61 MET cc_start: 0.4405 (mmt) cc_final: 0.3990 (tpp) REVERT: I 91 ARG cc_start: 0.6041 (mmm160) cc_final: 0.5472 (mmm160) REVERT: J 102 TYR cc_start: 0.7087 (m-80) cc_final: 0.6816 (m-80) REVERT: J 116 PHE cc_start: 0.6155 (t80) cc_final: 0.5934 (t80) REVERT: M 171 ASN cc_start: 0.8308 (t0) cc_final: 0.8011 (t0) REVERT: M 271 VAL cc_start: 0.7222 (OUTLIER) cc_final: 0.6992 (p) REVERT: M 294 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7567 (tt) outliers start: 34 outliers final: 20 residues processed: 137 average time/residue: 0.2015 time to fit residues: 38.8605 Evaluate side-chains 120 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain I residue 80 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 32 optimal weight: 0.6980 chunk 87 optimal weight: 0.0370 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN B 87 ASN ** H 98 GLN ** 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: 0.7231 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7582 Z= 0.203 Angle : 0.603 8.629 10289 Z= 0.293 Chirality : 0.040 0.193 1286 Planarity : 0.003 0.039 1259 Dihedral : 5.103 17.614 1064 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.92 % Allowed : 22.74 % Favored : 72.34 % 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: -0.93 (0.27), residues: 1015 helix: -0.41 (0.18), residues: 805 sheet: None (None), residues: 0 loop : -0.80 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 117 HIS 0.004 0.001 HIS M 248 PHE 0.025 0.002 PHE G 107 TYR 0.009 0.001 TYR N 88 ARG 0.002 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 151 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 114 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: C 81 MET cc_start: 0.7322 (tmt) cc_final: 0.6836 (tmt) REVERT: D 81 MET cc_start: 0.7328 (ttp) cc_final: 0.6628 (tmm) REVERT: D 110 THR cc_start: 0.6464 (m) cc_final: 0.6185 (p) REVERT: E 78 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.6034 (tp) REVERT: E 105 LEU cc_start: 0.4075 (tt) cc_final: 0.1812 (mt) REVERT: F 61 MET cc_start: 0.7668 (mmm) cc_final: 0.7041 (mpp) REVERT: G 81 MET cc_start: 0.7174 (tpt) cc_final: 0.6396 (tmm) REVERT: G 116 PHE cc_start: 0.5810 (OUTLIER) cc_final: 0.5266 (m-80) REVERT: H 61 MET cc_start: 0.6456 (mmm) cc_final: 0.5881 (mmm) REVERT: I 71 LEU cc_start: 0.7143 (tt) cc_final: 0.6821 (mt) REVERT: I 91 ARG cc_start: 0.5920 (mmm160) cc_final: 0.5339 (mmm160) REVERT: J 102 TYR cc_start: 0.7022 (m-80) cc_final: 0.6730 (m-80) REVERT: J 116 PHE cc_start: 0.6364 (t80) cc_final: 0.6072 (t80) REVERT: M 294 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7562 (tt) outliers start: 37 outliers final: 23 residues processed: 143 average time/residue: 0.1440 time to fit residues: 30.1052 Evaluate side-chains 127 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 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 125 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 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 294 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: 0.5980 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 96 optimal weight: 0.0670 chunk 80 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 0.1980 chunk 93 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 overall best weight: 0.2616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7582 Z= 0.184 Angle : 0.606 9.783 10289 Z= 0.290 Chirality : 0.039 0.184 1286 Planarity : 0.003 0.037 1259 Dihedral : 5.001 16.962 1064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.65 % Allowed : 23.80 % Favored : 71.54 % 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: -0.57 (0.27), residues: 1015 helix: -0.14 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.74 (0.49), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 117 HIS 0.003 0.001 HIS M 248 PHE 0.028 0.001 PHE G 107 TYR 0.009 0.001 TYR N 88 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 146 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 111 time to evaluate : 0.832 Fit side-chains REVERT: B 95 ILE cc_start: 0.3901 (tt) cc_final: 0.3551 (mt) REVERT: C 81 MET cc_start: 0.7329 (tmt) cc_final: 0.6888 (tmt) REVERT: D 81 MET cc_start: 0.7179 (ttp) cc_final: 0.6698 (tmm) REVERT: E 105 LEU cc_start: 0.4111 (OUTLIER) cc_final: 0.1938 (mt) REVERT: E 111 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6083 (mt-10) REVERT: F 61 MET cc_start: 0.7497 (mmm) cc_final: 0.6683 (mpp) REVERT: F 107 PHE cc_start: 0.6847 (t80) cc_final: 0.6406 (t80) REVERT: G 81 MET cc_start: 0.7132 (tpt) cc_final: 0.6483 (tmm) REVERT: G 99 LEU cc_start: 0.5602 (mt) cc_final: 0.5391 (mp) REVERT: G 116 PHE cc_start: 0.5663 (OUTLIER) cc_final: 0.5197 (m-80) REVERT: I 71 LEU cc_start: 0.7232 (tt) cc_final: 0.6807 (mt) REVERT: J 102 TYR cc_start: 0.7015 (m-80) cc_final: 0.6753 (m-80) REVERT: M 294 LEU cc_start: 0.8091 (tt) cc_final: 0.7772 (tt) outliers start: 35 outliers final: 27 residues processed: 141 average time/residue: 0.1498 time to fit residues: 30.4798 Evaluate side-chains 131 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 102 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 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 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 125 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 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 0.0030 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN D 98 GLN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7582 Z= 0.283 Angle : 0.700 10.100 10289 Z= 0.339 Chirality : 0.043 0.145 1286 Planarity : 0.004 0.044 1259 Dihedral : 5.477 17.523 1064 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.98 % Allowed : 22.74 % Favored : 71.28 % 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: -0.74 (0.27), residues: 1015 helix: -0.24 (0.19), residues: 803 sheet: None (None), residues: 0 loop : -0.90 (0.48), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 215 HIS 0.004 0.001 HIS M 248 PHE 0.030 0.002 PHE F 116 TYR 0.008 0.001 TYR M 114 ARG 0.003 0.000 ARG M 133 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 105 time to evaluate : 0.861 Fit side-chains REVERT: B 95 ILE cc_start: 0.4776 (tt) cc_final: 0.4360 (mt) REVERT: D 81 MET cc_start: 0.7178 (ttp) cc_final: 0.6785 (tmm) REVERT: E 105 LEU cc_start: 0.4856 (OUTLIER) cc_final: 0.4610 (tp) REVERT: F 61 MET cc_start: 0.7471 (mmm) cc_final: 0.6537 (mpp) REVERT: G 81 MET cc_start: 0.7045 (tpt) cc_final: 0.6672 (tmm) REVERT: G 116 PHE cc_start: 0.6075 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: H 61 MET cc_start: 0.6730 (mmm) cc_final: 0.6077 (mmm) REVERT: H 116 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.5486 (m-80) REVERT: I 91 ARG cc_start: 0.5764 (mmm160) cc_final: 0.5526 (mmm160) REVERT: J 102 TYR cc_start: 0.7321 (m-80) cc_final: 0.6928 (m-80) REVERT: J 116 PHE cc_start: 0.6853 (t80) cc_final: 0.6572 (t80) REVERT: M 294 LEU cc_start: 0.8183 (tt) cc_final: 0.7881 (tt) REVERT: M 316 ILE cc_start: 0.7580 (mp) cc_final: 0.7263 (mt) outliers start: 45 outliers final: 34 residues processed: 142 average time/residue: 0.1520 time to fit residues: 31.1458 Evaluate side-chains 133 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 96 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain 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 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.0570 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 75 optimal weight: 0.4980 chunk 87 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7582 Z= 0.237 Angle : 0.662 11.447 10289 Z= 0.316 Chirality : 0.041 0.158 1286 Planarity : 0.004 0.041 1259 Dihedral : 5.264 16.662 1064 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.45 % Allowed : 23.40 % Favored : 71.14 % 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: -0.54 (0.28), residues: 1015 helix: -0.10 (0.19), residues: 804 sheet: None (None), residues: 0 loop : -0.84 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 215 HIS 0.004 0.001 HIS M 248 PHE 0.034 0.002 PHE G 107 TYR 0.009 0.001 TYR N 88 ARG 0.001 0.000 ARG M 133 *********************** 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 141 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 100 time to evaluate : 0.850 Fit side-chains REVERT: D 81 MET cc_start: 0.7316 (ttp) cc_final: 0.6948 (tmm) REVERT: F 60 LYS cc_start: 0.7324 (mmtt) cc_final: 0.6405 (ttmt) REVERT: F 61 MET cc_start: 0.7420 (mmm) cc_final: 0.6805 (mpp) REVERT: G 116 PHE cc_start: 0.5975 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: H 61 MET cc_start: 0.6962 (mmm) cc_final: 0.6565 (mmm) REVERT: H 116 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5570 (m-80) REVERT: I 71 LEU cc_start: 0.7302 (tt) cc_final: 0.6881 (mt) REVERT: I 91 ARG cc_start: 0.5608 (mmm160) cc_final: 0.5358 (mmm160) REVERT: J 102 TYR cc_start: 0.7157 (m-80) cc_final: 0.6815 (m-80) REVERT: J 116 PHE cc_start: 0.6921 (t80) cc_final: 0.6698 (t80) REVERT: M 294 LEU cc_start: 0.8167 (tt) cc_final: 0.7863 (tt) outliers start: 41 outliers final: 34 residues processed: 135 average time/residue: 0.1514 time to fit residues: 29.5695 Evaluate side-chains 130 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain 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 85 LEU Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 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 154 THR Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.0000 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 0.2980 chunk 58 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 overall best weight: 0.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7582 Z= 0.212 Angle : 0.660 10.272 10289 Z= 0.310 Chirality : 0.041 0.201 1286 Planarity : 0.003 0.038 1259 Dihedral : 5.174 16.691 1064 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.45 % Allowed : 23.40 % Favored : 71.14 % 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: -0.39 (0.28), residues: 1015 helix: 0.03 (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 0.010 0.001 TRP M 215 HIS 0.003 0.001 HIS M 248 PHE 0.035 0.002 PHE G 107 TYR 0.011 0.001 TYR C 102 ARG 0.001 0.000 ARG J 91 *********************** 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 145 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 104 time to evaluate : 0.812 Fit side-chains REVERT: C 81 MET cc_start: 0.7286 (tmt) cc_final: 0.6885 (tmt) REVERT: D 81 MET cc_start: 0.7310 (ttp) cc_final: 0.6896 (tmm) REVERT: E 97 LYS cc_start: 0.5185 (mmtm) cc_final: 0.4667 (tppt) REVERT: F 60 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6385 (ttmt) REVERT: F 61 MET cc_start: 0.7331 (mmm) cc_final: 0.6905 (mpp) REVERT: G 81 MET cc_start: 0.6743 (tmm) cc_final: 0.6210 (tmm) REVERT: G 116 PHE cc_start: 0.6018 (OUTLIER) cc_final: 0.5538 (m-80) REVERT: H 61 MET cc_start: 0.6730 (mmm) cc_final: 0.6496 (mmm) REVERT: H 116 PHE cc_start: 0.5944 (OUTLIER) cc_final: 0.5499 (m-80) REVERT: I 71 LEU cc_start: 0.7288 (tt) cc_final: 0.6907 (mt) REVERT: I 91 ARG cc_start: 0.5576 (mmm160) cc_final: 0.5294 (mmm160) REVERT: J 82 PHE cc_start: 0.8115 (m-80) cc_final: 0.7472 (t80) REVERT: J 102 TYR cc_start: 0.7168 (m-80) cc_final: 0.6929 (m-80) REVERT: M 294 LEU cc_start: 0.8148 (tt) cc_final: 0.7855 (tt) outliers start: 41 outliers final: 35 residues processed: 139 average time/residue: 0.1616 time to fit residues: 32.5370 Evaluate side-chains 134 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 97 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 81 MET Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 8 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7582 Z= 0.207 Angle : 0.650 9.320 10289 Z= 0.306 Chirality : 0.041 0.186 1286 Planarity : 0.003 0.037 1259 Dihedral : 5.138 16.643 1064 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.32 % Allowed : 24.07 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.30 (0.28), residues: 1015 helix: 0.08 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.81 (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 0.036 0.002 PHE G 107 TYR 0.014 0.002 TYR C 102 ARG 0.001 0.000 ARG J 91 ********************** 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 134 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 0.795 Fit side-chains REVERT: C 81 MET cc_start: 0.7306 (tmt) cc_final: 0.6881 (tmt) REVERT: D 81 MET cc_start: 0.7245 (ttp) cc_final: 0.6859 (tmm) REVERT: E 97 LYS cc_start: 0.4946 (mmtm) cc_final: 0.4438 (tppt) REVERT: F 60 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6284 (ttpt) REVERT: F 61 MET cc_start: 0.7276 (mmm) cc_final: 0.6790 (mpp) REVERT: G 81 MET cc_start: 0.6641 (tmm) cc_final: 0.6110 (tmm) REVERT: G 116 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: H 116 PHE cc_start: 0.5921 (OUTLIER) cc_final: 0.5462 (m-80) REVERT: I 71 LEU cc_start: 0.7298 (tt) cc_final: 0.6900 (mt) REVERT: I 91 ARG cc_start: 0.5554 (mmm160) cc_final: 0.5257 (mmm160) REVERT: J 56 LEU cc_start: 0.6750 (mt) cc_final: 0.6420 (tp) REVERT: J 82 PHE cc_start: 0.7993 (m-80) cc_final: 0.7436 (t80) REVERT: J 102 TYR cc_start: 0.7409 (m-80) cc_final: 0.7060 (m-80) REVERT: M 294 LEU cc_start: 0.8151 (tt) cc_final: 0.7868 (tt) outliers start: 40 outliers final: 35 residues processed: 128 average time/residue: 0.1753 time to fit residues: 31.8426 Evaluate side-chains 130 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 93 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain 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 105 LEU Chi-restraints excluded: chain F residue 110 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 116 PHE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 116 PHE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 167 LEU Chi-restraints excluded: chain M residue 249 THR Chi-restraints excluded: chain M residue 265 LEU Chi-restraints excluded: chain M residue 271 VAL Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain N residue 84 SER Chi-restraints excluded: chain N residue 88 TYR Chi-restraints excluded: chain N residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 33 optimal weight: 0.2980 chunk 81 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 69 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 87 ASN ** G 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.129148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 124)---------------| | r_work = 0.3881 r_free = 0.3881 target = 0.114062 restraints weight = 19890.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.112229 restraints weight = 19844.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112727 restraints weight = 15158.558| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7582 Z= 0.244 Angle : 0.677 11.926 10289 Z= 0.322 Chirality : 0.042 0.160 1286 Planarity : 0.004 0.038 1259 Dihedral : 5.261 16.341 1064 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.32 % Allowed : 24.34 % Favored : 70.35 % 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: -0.46 (0.27), residues: 1015 helix: -0.01 (0.19), residues: 805 sheet: None (None), residues: 0 loop : -0.94 (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 252 PHE 0.025 0.002 PHE F 116 TYR 0.015 0.002 TYR C 102 ARG 0.001 0.000 ARG M 239 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.80 seconds wall clock time: 36 minutes 57.44 seconds (2217.44 seconds total)