Starting phenix.real_space_refine on Thu Feb 15 23:43:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6v_29785/02_2024/8g6v_29785.pdb" } resolution = 3.4 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= 0.001 sd= 0.006 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 72 5.16 5 C 8932 2.51 5 N 2248 2.21 5 O 2484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 32": "OD1" <-> "OD2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "D ASP 4": "OD1" <-> "OD2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "E ASP 4": "OD1" <-> "OD2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E ASP 32": "OD1" <-> "OD2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "G ASP 4": "OD1" <-> "OD2" Residue "G GLU 14": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 117": "OE1" <-> "OE2" Residue "F ASP 22": "OD1" <-> "OD2" Residue "F ASP 32": "OD1" <-> "OD2" Residue "F GLU 117": "OE1" <-> "OE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 32": "OD1" <-> "OD2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "J GLU 14": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J GLU 117": "OE1" <-> "OE2" Residue "L ASP 22": "OD1" <-> "OD2" Residue "L PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13736 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "A" Number of atoms: 1155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Conformer: "B" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} bond proxies already assigned to first conformer: 1167 Chain: "C" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "D" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "E" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "G" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "F" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "H" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1129 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 11, 'TRANS': 129} Chain: "K" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1136 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 11, 'TRANS': 130} Chain: "J" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1144 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "L" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1151 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 112 " occ=0.12 ... (20 atoms not shown) pdb=" NH2BARG A 112 " occ=0.88 Time building chain proxies: 8.19, per 1000 atoms: 0.60 Number of scatterers: 13736 At special positions: 0 Unit cell: (178.08, 181.44, 72.8, 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 72 16.00 O 2484 8.00 N 2248 7.00 C 8932 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS D 61 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS G 61 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS H 61 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS K 61 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS L 61 " distance=2.02 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: 4.90 Conformation dependent library (CDL) restraints added in 2.5 seconds 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3290 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 0 sheets defined 74.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 26 through 38 removed outlier: 3.754A pdb=" N ASP B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 49 through 75 removed outlier: 3.746A pdb=" N THR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 54 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 111 removed outlier: 4.654A pdb=" N MET B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS B 96 " --> pdb=" O ASN B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 128 removed outlier: 3.591A pdb=" N VAL B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 128 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 17 Processing helix chain 'A' and resid 26 through 38 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 49 through 76 removed outlier: 3.595A pdb=" N GLN A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 110 removed outlier: 5.678A pdb=" N GLY A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N PHE A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 128 removed outlier: 3.600A pdb=" N VAL A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 18 through 19 No H-bonds generated for 'chain 'C' and resid 18 through 19' Processing helix chain 'C' and resid 20 through 24 removed outlier: 3.931A pdb=" N PHE C 24 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 39 removed outlier: 3.623A pdb=" N LEU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.775A pdb=" N SER C 44 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 75 removed outlier: 3.812A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 54 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 55 " --> pdb=" O HIS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 111 removed outlier: 4.729A pdb=" N GLY C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS C 96 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 26 through 43 removed outlier: 3.813A pdb=" N ARG D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N GLU D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.743A pdb=" N THR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 54 " --> pdb=" O PRO D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 93 Processing helix chain 'D' and resid 94 through 111 Processing helix chain 'D' and resid 111 through 128 removed outlier: 3.775A pdb=" N VAL D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 133 removed outlier: 3.563A pdb=" N ARG D 133 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 17 Processing helix chain 'E' and resid 18 through 19 No H-bonds generated for 'chain 'E' and resid 18 through 19' Processing helix chain 'E' and resid 20 through 24 removed outlier: 4.071A pdb=" N PHE E 24 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 39 removed outlier: 3.507A pdb=" N LEU E 37 " --> pdb=" O THR E 33 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 75 Processing helix chain 'E' and resid 78 through 93 removed outlier: 3.710A pdb=" N VAL E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.903A pdb=" N PHE E 97 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'G' and resid 12 through 17 Processing helix chain 'G' and resid 26 through 43 removed outlier: 3.787A pdb=" N ARG G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLU G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 78 through 111 removed outlier: 3.547A pdb=" N ARG G 82 " --> pdb=" O ASP G 78 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY G 94 " --> pdb=" O ASN G 90 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE G 97 " --> pdb=" O MET G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 128 removed outlier: 3.743A pdb=" N GLU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 133 removed outlier: 3.533A pdb=" N ARG G 133 " --> pdb=" O PRO G 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 17 Processing helix chain 'F' and resid 26 through 43 removed outlier: 3.788A pdb=" N ARG F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.753A pdb=" N THR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 54 " --> pdb=" O PRO F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 111 removed outlier: 4.663A pdb=" N GLY F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LYS F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N PHE F 97 " --> pdb=" O MET F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 128 removed outlier: 3.868A pdb=" N VAL F 120 " --> pdb=" O ILE F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 133 removed outlier: 3.564A pdb=" N ARG F 133 " --> pdb=" O PRO F 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 17 Processing helix chain 'H' and resid 18 through 19 No H-bonds generated for 'chain 'H' and resid 18 through 19' Processing helix chain 'H' and resid 20 through 24 removed outlier: 3.689A pdb=" N PHE H 24 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 38 removed outlier: 3.570A pdb=" N LEU H 30 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 Processing helix chain 'H' and resid 49 through 75 removed outlier: 3.505A pdb=" N GLN H 57 " --> pdb=" O THR H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 93 Processing helix chain 'H' and resid 93 through 111 removed outlier: 4.131A pdb=" N PHE H 97 " --> pdb=" O MET H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 128 removed outlier: 3.660A pdb=" N THR H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 10 Processing helix chain 'I' and resid 12 through 17 Processing helix chain 'I' and resid 26 through 38 Processing helix chain 'I' and resid 38 through 44 Processing helix chain 'I' and resid 49 through 76 removed outlier: 3.969A pdb=" N THR I 53 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU I 55 " --> pdb=" O HIS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 111 removed outlier: 3.553A pdb=" N LEU I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS I 96 " --> pdb=" O ASN I 92 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE I 97 " --> pdb=" O MET I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 127 Processing helix chain 'K' and resid 12 through 17 Processing helix chain 'K' and resid 26 through 38 Processing helix chain 'K' and resid 38 through 43 Processing helix chain 'K' and resid 49 through 76 removed outlier: 3.571A pdb=" N GLN K 57 " --> pdb=" O THR K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 110 removed outlier: 3.629A pdb=" N ASP K 83 " --> pdb=" O PRO K 79 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLY K 94 " --> pdb=" O ASN K 90 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS K 96 " --> pdb=" O ASN K 92 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 128 removed outlier: 3.707A pdb=" N THR K 128 " --> pdb=" O VAL K 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 17 Processing helix chain 'J' and resid 26 through 43 removed outlier: 4.011A pdb=" N ASP J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLU J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ALA J 41 " --> pdb=" O LEU J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 76 removed outlier: 3.749A pdb=" N THR J 53 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA J 54 " --> pdb=" O PRO J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 110 removed outlier: 3.732A pdb=" N VAL J 86 " --> pdb=" O ARG J 82 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY J 94 " --> pdb=" O ASN J 90 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS J 96 " --> pdb=" O ASN J 92 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE J 97 " --> pdb=" O MET J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 128 removed outlier: 3.574A pdb=" N ARG J 127 " --> pdb=" O GLY J 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 17 Processing helix chain 'L' and resid 26 through 36 Processing helix chain 'L' and resid 49 through 75 removed outlier: 3.530A pdb=" N GLN L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU L 65 " --> pdb=" O CYS L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 93 Processing helix chain 'L' and resid 93 through 111 removed outlier: 3.699A pdb=" N PHE L 97 " --> pdb=" O MET L 93 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 108 " --> pdb=" O HIS L 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 128 removed outlier: 3.615A pdb=" N THR L 128 " --> pdb=" O VAL L 124 " (cutoff:3.500A) 869 hydrogen bonds defined for protein. 2580 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: 3.69 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.47: 3605 1.47 - 1.59: 6122 1.59 - 1.72: 1 1.72 - 1.85: 108 Bond restraints: 14161 Sorted by residual: bond pdb=" CB PRO L 144 " pdb=" CG PRO L 144 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" CG PRO E 144 " pdb=" CD PRO E 144 " ideal model delta sigma weight residual 1.503 1.574 -0.071 3.40e-02 8.65e+02 4.30e+00 bond pdb=" CB PRO E 144 " pdb=" CG PRO E 144 " ideal model delta sigma weight residual 1.492 1.576 -0.084 5.00e-02 4.00e+02 2.82e+00 bond pdb=" CB PRO E 79 " pdb=" CG PRO E 79 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.42e+00 bond pdb=" CG PRO L 144 " pdb=" CD PRO L 144 " ideal model delta sigma weight residual 1.503 1.555 -0.052 3.40e-02 8.65e+02 2.30e+00 ... (remaining 14156 not shown) Histogram of bond angle deviations from ideal: 100.23 - 107.00: 664 107.00 - 113.77: 7826 113.77 - 120.55: 5812 120.55 - 127.32: 4844 127.32 - 134.10: 244 Bond angle restraints: 19390 Sorted by residual: angle pdb=" CA PRO L 144 " pdb=" N PRO L 144 " pdb=" CD PRO L 144 " ideal model delta sigma weight residual 112.00 104.87 7.13 1.40e+00 5.10e-01 2.59e+01 angle pdb=" CA LEU J 84 " pdb=" CB LEU J 84 " pdb=" CG LEU J 84 " ideal model delta sigma weight residual 116.30 132.30 -16.00 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CA PRO E 79 " pdb=" N PRO E 79 " pdb=" CD PRO E 79 " ideal model delta sigma weight residual 112.00 105.75 6.25 1.40e+00 5.10e-01 1.99e+01 angle pdb=" CA LEU G 84 " pdb=" CB LEU G 84 " pdb=" CG LEU G 84 " ideal model delta sigma weight residual 116.30 130.33 -14.03 3.50e+00 8.16e-02 1.61e+01 angle pdb=" CA PRO E 144 " pdb=" N PRO E 144 " pdb=" CD PRO E 144 " ideal model delta sigma weight residual 112.00 106.97 5.03 1.40e+00 5.10e-01 1.29e+01 ... (remaining 19385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 7114 17.50 - 35.00: 962 35.00 - 52.50: 250 52.50 - 70.00: 22 70.00 - 87.50: 9 Dihedral angle restraints: 8357 sinusoidal: 3301 harmonic: 5056 Sorted by residual: dihedral pdb=" CB CYS C 61 " pdb=" SG CYS C 61 " pdb=" SG CYS D 61 " pdb=" CB CYS D 61 " ideal model delta sinusoidal sigma weight residual -86.00 -154.12 68.12 1 1.00e+01 1.00e-02 6.02e+01 dihedral pdb=" CA ASN J 90 " pdb=" C ASN J 90 " pdb=" N THR J 91 " pdb=" CA THR J 91 " ideal model delta harmonic sigma weight residual 180.00 144.79 35.21 0 5.00e+00 4.00e-02 4.96e+01 dihedral pdb=" CA ASN K 90 " pdb=" C ASN K 90 " pdb=" N THR K 91 " pdb=" CA THR K 91 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 8354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1434 0.031 - 0.062: 545 0.062 - 0.092: 147 0.092 - 0.123: 62 0.123 - 0.154: 5 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CB VAL H 86 " pdb=" CA VAL H 86 " pdb=" CG1 VAL H 86 " pdb=" CG2 VAL H 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ASN G 90 " pdb=" N ASN G 90 " pdb=" C ASN G 90 " pdb=" CB ASN G 90 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ASN A 90 " pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CB ASN A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 2190 not shown) Planarity restraints: 2455 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 78 " -0.093 5.00e-02 4.00e+02 1.38e-01 3.04e+01 pdb=" N PRO E 79 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO E 79 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO E 79 " -0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 78 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO C 79 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 79 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 79 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 89 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C VAL H 89 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL H 89 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN H 90 " -0.011 2.00e-02 2.50e+03 ... (remaining 2452 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 131 2.65 - 3.21: 12290 3.21 - 3.77: 21390 3.77 - 4.34: 27868 4.34 - 4.90: 47630 Nonbonded interactions: 109309 Sorted by model distance: nonbonded pdb=" OG SER K 26 " pdb=" OD1 ASP K 29 " model vdw 2.084 2.440 nonbonded pdb=" OG SER A 26 " pdb=" OD1 ASP A 29 " model vdw 2.148 2.440 nonbonded pdb=" OD2 ASP G 78 " pdb=" OG SER G 81 " model vdw 2.224 2.440 nonbonded pdb=" OD2 ASP F 78 " pdb=" OG SER F 81 " model vdw 2.276 2.440 nonbonded pdb=" OD2 ASP D 78 " pdb=" OG SER D 81 " model vdw 2.304 2.440 ... (remaining 109304 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' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'B' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'C' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'D' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'E' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'F' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'G' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'H' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'I' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'J' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'K' and (resid 1 through 111 or resid 113 through 141)) selection = (chain 'L' and (resid 1 through 111 or resid 113 through 141)) } 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=0.12 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.210 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: 0.020 Extract box with map and model: 18.750 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.280 Find NCS groups from input model: 1.060 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 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 : 0.003 0.118 14161 Z= 0.193 Angle : 0.596 15.996 19390 Z= 0.312 Chirality : 0.037 0.154 2193 Planarity : 0.006 0.138 2455 Dihedral : 16.349 87.499 5052 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.85 % Allowed : 24.72 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.60 (0.21), residues: 1695 helix: 1.40 (0.15), residues: 1221 sheet: None (None), residues: 0 loop : 0.40 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 71 HIS 0.007 0.001 HIS B 47 PHE 0.009 0.001 PHE F 122 TYR 0.013 0.001 TYR J 132 ARG 0.010 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 373 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ASN cc_start: 0.8616 (t0) cc_final: 0.8205 (t0) REVERT: G 82 ARG cc_start: 0.7999 (ttp-110) cc_final: 0.7637 (mtp85) REVERT: F 64 GLU cc_start: 0.7802 (tp30) cc_final: 0.7407 (tp30) REVERT: F 91 THR cc_start: 0.8407 (m) cc_final: 0.8205 (p) REVERT: H 93 MET cc_start: 0.7758 (mmt) cc_final: 0.6627 (mmt) REVERT: I 78 ASP cc_start: 0.7274 (t70) cc_final: 0.6995 (t70) REVERT: K 75 ASN cc_start: 0.8385 (t0) cc_final: 0.8173 (t0) REVERT: L 127 ARG cc_start: 0.6821 (tpt170) cc_final: 0.4823 (tmt-80) outliers start: 12 outliers final: 5 residues processed: 376 average time/residue: 0.2592 time to fit residues: 139.0407 Evaluate side-chains 369 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 364 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain H residue 66 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 98 optimal weight: 0.0670 chunk 152 optimal weight: 0.0770 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 14161 Z= 0.141 Angle : 0.497 10.618 19390 Z= 0.245 Chirality : 0.036 0.134 2193 Planarity : 0.005 0.078 2455 Dihedral : 4.186 44.616 1875 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.36 % Allowed : 23.93 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.09 (0.21), residues: 1695 helix: 1.78 (0.15), residues: 1216 sheet: None (None), residues: 0 loop : 0.53 (0.31), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 71 HIS 0.004 0.001 HIS B 47 PHE 0.010 0.001 PHE K 97 TYR 0.009 0.001 TYR I 88 ARG 0.007 0.000 ARG J 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 370 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8075 (tpm170) REVERT: D 82 ARG cc_start: 0.8219 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: G 82 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7584 (mtp85) REVERT: F 18 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8466 (t80) REVERT: F 64 GLU cc_start: 0.7866 (tp30) cc_final: 0.7505 (mt-10) REVERT: F 91 THR cc_start: 0.8400 (m) cc_final: 0.8196 (p) REVERT: F 96 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8407 (ptmt) REVERT: I 78 ASP cc_start: 0.7362 (t70) cc_final: 0.7024 (t70) REVERT: K 75 ASN cc_start: 0.8304 (t0) cc_final: 0.8082 (t0) REVERT: L 127 ARG cc_start: 0.6847 (tpt170) cc_final: 0.4835 (tmt-80) outliers start: 35 outliers final: 14 residues processed: 387 average time/residue: 0.2534 time to fit residues: 141.1831 Evaluate side-chains 368 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 353 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14161 Z= 0.321 Angle : 0.577 11.502 19390 Z= 0.289 Chirality : 0.041 0.145 2193 Planarity : 0.006 0.066 2455 Dihedral : 3.943 32.343 1863 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.54 % Allowed : 23.54 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1.90 (0.21), residues: 1695 helix: 1.70 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.24 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 71 HIS 0.008 0.002 HIS B 47 PHE 0.019 0.001 PHE K 97 TYR 0.009 0.001 TYR I 118 ARG 0.003 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 365 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8390 (tpp-160) cc_final: 0.8074 (tpm170) REVERT: B 61 CYS cc_start: 0.8383 (m) cc_final: 0.7960 (t) REVERT: G 77 GLU cc_start: 0.5772 (pm20) cc_final: 0.5541 (pm20) REVERT: G 82 ARG cc_start: 0.8165 (ttp-110) cc_final: 0.7735 (mtp85) REVERT: F 18 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8476 (t80) REVERT: F 64 GLU cc_start: 0.7844 (tp30) cc_final: 0.7455 (mt-10) REVERT: F 91 THR cc_start: 0.8552 (m) cc_final: 0.8243 (p) REVERT: K 75 ASN cc_start: 0.8500 (t0) cc_final: 0.8247 (t0) outliers start: 53 outliers final: 38 residues processed: 391 average time/residue: 0.2563 time to fit residues: 144.3171 Evaluate side-chains 391 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 352 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 50.0000 chunk 153 optimal weight: 0.0030 chunk 162 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14161 Z= 0.144 Angle : 0.490 11.569 19390 Z= 0.243 Chirality : 0.037 0.144 2193 Planarity : 0.005 0.056 2455 Dihedral : 3.750 34.030 1863 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.28 % Allowed : 24.07 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.23 (0.21), residues: 1695 helix: 1.92 (0.15), residues: 1220 sheet: None (None), residues: 0 loop : 0.46 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 71 HIS 0.004 0.001 HIS B 47 PHE 0.014 0.001 PHE K 97 TYR 0.006 0.001 TYR A 88 ARG 0.003 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 358 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8395 (tpp-160) cc_final: 0.8042 (tpm170) REVERT: B 61 CYS cc_start: 0.8347 (m) cc_final: 0.7962 (t) REVERT: C 76 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6565 (mp) REVERT: D 18 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8431 (t80) REVERT: G 82 ARG cc_start: 0.8101 (ttp-110) cc_final: 0.7595 (mtp85) REVERT: F 18 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8600 (t80) REVERT: F 64 GLU cc_start: 0.7745 (tp30) cc_final: 0.7451 (mt-10) REVERT: F 91 THR cc_start: 0.8490 (m) cc_final: 0.8216 (p) REVERT: F 96 LYS cc_start: 0.8830 (ptpt) cc_final: 0.8533 (ptmt) REVERT: K 75 ASN cc_start: 0.8461 (t0) cc_final: 0.8224 (t0) REVERT: J 96 LYS cc_start: 0.8678 (ptmt) cc_final: 0.8442 (ptmt) REVERT: L 91 THR cc_start: 0.8643 (m) cc_final: 0.8384 (m) outliers start: 49 outliers final: 29 residues processed: 385 average time/residue: 0.2485 time to fit residues: 137.6208 Evaluate side-chains 382 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 350 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14161 Z= 0.198 Angle : 0.508 11.265 19390 Z= 0.254 Chirality : 0.038 0.147 2193 Planarity : 0.005 0.051 2455 Dihedral : 3.753 33.520 1863 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.67 % Allowed : 23.80 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.32 (0.21), residues: 1695 helix: 1.99 (0.15), residues: 1218 sheet: None (None), residues: 0 loop : 0.48 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 71 HIS 0.006 0.001 HIS B 47 PHE 0.016 0.001 PHE K 97 TYR 0.008 0.001 TYR K 88 ARG 0.004 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 360 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ARG cc_start: 0.8361 (tpp-160) cc_final: 0.8012 (tpm170) REVERT: B 61 CYS cc_start: 0.8352 (m) cc_final: 0.7992 (t) REVERT: C 76 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6558 (mp) REVERT: D 18 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8510 (t80) REVERT: G 82 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7628 (mtp85) REVERT: F 16 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8588 (mp) REVERT: F 18 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8587 (t80) REVERT: F 64 GLU cc_start: 0.7760 (tp30) cc_final: 0.7406 (mt-10) REVERT: F 91 THR cc_start: 0.8512 (m) cc_final: 0.8227 (p) REVERT: F 96 LYS cc_start: 0.8871 (ptpt) cc_final: 0.8515 (ptmt) REVERT: K 75 ASN cc_start: 0.8460 (t0) cc_final: 0.8216 (t0) REVERT: L 91 THR cc_start: 0.8675 (m) cc_final: 0.8422 (m) outliers start: 55 outliers final: 41 residues processed: 392 average time/residue: 0.2497 time to fit residues: 140.4915 Evaluate side-chains 397 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 352 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 ASN F 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14161 Z= 0.233 Angle : 0.525 11.296 19390 Z= 0.263 Chirality : 0.039 0.148 2193 Planarity : 0.005 0.048 2455 Dihedral : 3.818 33.472 1863 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.00 % Allowed : 23.67 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.25 (0.21), residues: 1695 helix: 1.96 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.38 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 71 HIS 0.006 0.001 HIS B 47 PHE 0.016 0.001 PHE K 97 TYR 0.009 0.001 TYR K 88 ARG 0.004 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 359 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.6294 (mtm) REVERT: B 28 ARG cc_start: 0.8375 (tpp-160) cc_final: 0.8038 (tpm170) REVERT: B 61 CYS cc_start: 0.8349 (m) cc_final: 0.7984 (t) REVERT: C 76 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6505 (mp) REVERT: D 16 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8588 (mp) REVERT: D 18 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8500 (t80) REVERT: G 82 ARG cc_start: 0.8138 (ttp-110) cc_final: 0.7860 (mtm-85) REVERT: F 16 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8636 (mp) REVERT: F 18 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8586 (t80) REVERT: F 64 GLU cc_start: 0.7744 (tp30) cc_final: 0.7403 (mt-10) REVERT: F 91 THR cc_start: 0.8531 (m) cc_final: 0.8229 (p) REVERT: F 96 LYS cc_start: 0.8895 (ptpt) cc_final: 0.8541 (ptmt) REVERT: K 75 ASN cc_start: 0.8488 (t0) cc_final: 0.8242 (t0) REVERT: J 96 LYS cc_start: 0.8752 (ptmt) cc_final: 0.8485 (ptmt) REVERT: L 91 THR cc_start: 0.8713 (m) cc_final: 0.8444 (m) outliers start: 60 outliers final: 45 residues processed: 395 average time/residue: 0.2523 time to fit residues: 143.0258 Evaluate side-chains 406 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 355 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 40.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS D 90 ASN F 90 ASN K 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14161 Z= 0.340 Angle : 0.590 11.267 19390 Z= 0.297 Chirality : 0.042 0.156 2193 Planarity : 0.006 0.047 2455 Dihedral : 4.037 32.439 1863 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.13 % Allowed : 23.74 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.02 (0.21), residues: 1695 helix: 1.83 (0.15), residues: 1224 sheet: None (None), residues: 0 loop : 0.13 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 71 HIS 0.007 0.002 HIS B 47 PHE 0.019 0.001 PHE K 97 TYR 0.010 0.001 TYR K 88 ARG 0.004 0.000 ARG H 127 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 357 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: B 28 ARG cc_start: 0.8367 (tpp-160) cc_final: 0.8061 (tpm170) REVERT: B 61 CYS cc_start: 0.8341 (m) cc_final: 0.8086 (t) REVERT: C 76 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6499 (mp) REVERT: D 16 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8714 (mp) REVERT: D 18 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8546 (t80) REVERT: E 75 ASN cc_start: 0.7741 (t0) cc_final: 0.7452 (t0) REVERT: G 82 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7830 (mtm-85) REVERT: F 16 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8697 (mp) REVERT: F 18 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8606 (t80) REVERT: F 64 GLU cc_start: 0.7754 (tp30) cc_final: 0.7373 (mt-10) REVERT: F 91 THR cc_start: 0.8546 (m) cc_final: 0.8222 (p) REVERT: F 96 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8565 (ptmt) REVERT: K 75 ASN cc_start: 0.8483 (t0) cc_final: 0.8212 (t0) REVERT: J 133 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8116 (ptp90) outliers start: 62 outliers final: 47 residues processed: 393 average time/residue: 0.2535 time to fit residues: 142.8235 Evaluate side-chains 410 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 356 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 61 CYS Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 12 THR Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN G 99 GLN F 90 ASN K 99 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14161 Z= 0.203 Angle : 0.534 12.040 19390 Z= 0.269 Chirality : 0.039 0.156 2193 Planarity : 0.005 0.046 2455 Dihedral : 3.932 33.736 1863 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.74 % Allowed : 24.33 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.20 (0.21), residues: 1695 helix: 1.95 (0.15), residues: 1223 sheet: None (None), residues: 0 loop : 0.29 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 71 HIS 0.005 0.001 HIS E 47 PHE 0.014 0.001 PHE K 97 TYR 0.009 0.001 TYR K 88 ARG 0.006 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8315 (m) cc_final: 0.8044 (t) REVERT: C 76 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6464 (mp) REVERT: D 16 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8602 (mp) REVERT: D 18 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8504 (t80) REVERT: D 84 LEU cc_start: 0.8393 (mt) cc_final: 0.8085 (mp) REVERT: E 29 ASP cc_start: 0.9102 (m-30) cc_final: 0.8773 (m-30) REVERT: G 82 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7792 (mtm-85) REVERT: F 16 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8575 (mp) REVERT: F 18 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8582 (t80) REVERT: F 64 GLU cc_start: 0.7729 (tp30) cc_final: 0.7394 (mt-10) REVERT: F 91 THR cc_start: 0.8525 (m) cc_final: 0.8243 (p) REVERT: F 96 LYS cc_start: 0.8870 (ptpt) cc_final: 0.8526 (ptmt) REVERT: K 75 ASN cc_start: 0.8474 (t0) cc_final: 0.8214 (t0) REVERT: J 96 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8454 (ptmt) REVERT: J 133 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8002 (ptp90) REVERT: L 91 THR cc_start: 0.8717 (m) cc_final: 0.8462 (m) outliers start: 56 outliers final: 44 residues processed: 388 average time/residue: 0.2515 time to fit residues: 140.3341 Evaluate side-chains 401 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 351 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 6 TYR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 72 VAL Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 136 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14161 Z= 0.180 Angle : 0.526 11.419 19390 Z= 0.263 Chirality : 0.038 0.156 2193 Planarity : 0.005 0.045 2455 Dihedral : 3.837 34.391 1863 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.41 % Allowed : 24.59 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.39 (0.21), residues: 1695 helix: 2.06 (0.15), residues: 1219 sheet: None (None), residues: 0 loop : 0.45 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 71 HIS 0.004 0.001 HIS E 47 PHE 0.014 0.001 PHE K 97 TYR 0.009 0.001 TYR J 132 ARG 0.005 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 355 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8319 (m) cc_final: 0.8057 (t) REVERT: C 76 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6437 (mp) REVERT: D 16 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8538 (mp) REVERT: D 18 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8567 (t80) REVERT: D 84 LEU cc_start: 0.8399 (mt) cc_final: 0.8097 (mp) REVERT: E 29 ASP cc_start: 0.9040 (m-30) cc_final: 0.8729 (m-30) REVERT: G 82 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7801 (mtm-85) REVERT: F 16 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8561 (mp) REVERT: F 18 PHE cc_start: 0.9147 (OUTLIER) cc_final: 0.8578 (t80) REVERT: F 64 GLU cc_start: 0.7835 (tp30) cc_final: 0.7416 (mt-10) REVERT: F 91 THR cc_start: 0.8502 (m) cc_final: 0.8250 (p) REVERT: F 96 LYS cc_start: 0.8842 (ptpt) cc_final: 0.8587 (ptmt) REVERT: K 75 ASN cc_start: 0.8426 (t0) cc_final: 0.8184 (t0) REVERT: J 96 LYS cc_start: 0.8698 (ptmt) cc_final: 0.8410 (ptmt) REVERT: L 29 ASP cc_start: 0.9074 (m-30) cc_final: 0.8746 (m-30) REVERT: L 91 THR cc_start: 0.8705 (m) cc_final: 0.8453 (m) outliers start: 51 outliers final: 42 residues processed: 386 average time/residue: 0.2599 time to fit residues: 144.4109 Evaluate side-chains 397 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 96 LYS Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 107 CYS Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 110 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 102 optimal weight: 40.0000 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14161 Z= 0.169 Angle : 0.520 11.403 19390 Z= 0.260 Chirality : 0.038 0.154 2193 Planarity : 0.005 0.044 2455 Dihedral : 3.761 34.022 1863 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.02 % Allowed : 25.18 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.49 (0.21), residues: 1695 helix: 2.13 (0.15), residues: 1214 sheet: None (None), residues: 0 loop : 0.53 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 PHE 0.014 0.001 PHE K 97 TYR 0.007 0.001 TYR K 88 ARG 0.005 0.000 ARG F 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3390 Ramachandran restraints generated. 1695 Oldfield, 0 Emsley, 1695 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 355 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 CYS cc_start: 0.8347 (m) cc_final: 0.8083 (t) REVERT: C 76 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6409 (mp) REVERT: D 16 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8481 (mp) REVERT: D 18 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8548 (t80) REVERT: D 84 LEU cc_start: 0.8397 (mt) cc_final: 0.8083 (mp) REVERT: E 29 ASP cc_start: 0.8992 (m-30) cc_final: 0.8701 (m-30) REVERT: G 82 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7824 (mtm-85) REVERT: F 16 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8498 (mp) REVERT: F 18 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8579 (t80) REVERT: F 64 GLU cc_start: 0.7867 (tp30) cc_final: 0.7430 (mt-10) REVERT: F 91 THR cc_start: 0.8483 (m) cc_final: 0.8246 (p) REVERT: F 96 LYS cc_start: 0.8835 (ptpt) cc_final: 0.8598 (ptmt) REVERT: H 93 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8054 (mpp) REVERT: K 75 ASN cc_start: 0.8393 (t0) cc_final: 0.8140 (t0) REVERT: J 71 TRP cc_start: 0.8385 (t60) cc_final: 0.7964 (t60) REVERT: J 84 LEU cc_start: 0.8219 (mt) cc_final: 0.7937 (mp) REVERT: J 96 LYS cc_start: 0.8696 (ptmt) cc_final: 0.8494 (ptmt) REVERT: J 133 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7875 (ptp90) REVERT: L 91 THR cc_start: 0.8733 (m) cc_final: 0.8498 (m) outliers start: 45 outliers final: 36 residues processed: 383 average time/residue: 0.2706 time to fit residues: 147.9739 Evaluate side-chains 392 residues out of total 1523 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 349 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain E residue 66 MET Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 PHE Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 66 MET Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 89 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain K residue 8 GLU Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 133 ARG Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 136 ASN Chi-restraints excluded: chain L residue 139 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.094793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.072664 restraints weight = 45009.089| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.53 r_work: 0.2465 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2507 r_free = 0.2507 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 14161 Z= 0.215 Angle : 0.765 59.199 19390 Z= 0.436 Chirality : 0.039 0.362 2193 Planarity : 0.005 0.044 2455 Dihedral : 3.761 34.020 1863 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.95 % Allowed : 25.51 % Favored : 71.54 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 2.49 (0.21), residues: 1695 helix: 2.13 (0.15), residues: 1214 sheet: None (None), residues: 0 loop : 0.54 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 71 HIS 0.004 0.001 HIS J 104 PHE 0.013 0.001 PHE K 97 TYR 0.017 0.001 TYR B 88 ARG 0.004 0.000 ARG F 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3500.87 seconds wall clock time: 63 minutes 49.03 seconds (3829.03 seconds total)