Starting phenix.real_space_refine on Sun Mar 17 05:52:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v9a_31813/03_2024/7v9a_31813.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 146 5.49 5 S 86 5.16 5 C 10128 2.51 5 N 2999 2.21 5 O 3517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ASP 378": "OD1" <-> "OD2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B ASP 448": "OD1" <-> "OD2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 138": "NH1" <-> "NH2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ASP 258": "OD1" <-> "OD2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C GLU 341": "OE1" <-> "OE2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 399": "OD1" <-> "OD2" Residue "C TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 114": "OD1" <-> "OD2" Residue "D PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 122": "OD1" <-> "OD2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "F TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 65": "NH1" <-> "NH2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "G ASP 125": "OD1" <-> "OD2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "G ARG 138": "NH1" <-> "NH2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G ARG 183": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 197": "NH1" <-> "NH2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 248": "NH1" <-> "NH2" Residue "G ASP 258": "OD1" <-> "OD2" Residue "G GLU 279": "OE1" <-> "OE2" Residue "G ARG 298": "NH1" <-> "NH2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G GLU 324": "OE1" <-> "OE2" Residue "G ASP 325": "OD1" <-> "OD2" Residue "G GLU 341": "OE1" <-> "OE2" Residue "G ARG 373": "NH1" <-> "NH2" Residue "G ASP 374": "OD1" <-> "OD2" Residue "G TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 21": "OE1" <-> "OE2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 66": "OE1" <-> "OE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16876 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2938 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 25, 'TRANS': 351} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3118 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 16, 'TRANS': 376} Chain: "D" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "E" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1031 Classifications: {'peptide': 129} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 526 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "G" Number of atoms: 2762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2762 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 13, 'TRANS': 335} Chain: "H" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 9, 'TRANS': 88} Chain: "I" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 123} Chain: "J" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 541 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "R" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3144 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 70, 'rna3p_pyr': 57} Link IDs: {'rna2p': 19, 'rna3p': 126} Chain breaks: 2 Time building chain proxies: 9.26, per 1000 atoms: 0.55 Number of scatterers: 16876 At special positions: 0 Unit cell: (183.7, 96.8, 132, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 146 15.00 O 3517 8.00 N 2999 7.00 C 10128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.75 Conformation dependent library (CDL) restraints added in 2.6 seconds 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 21 sheets defined 24.7% alpha, 23.0% beta 16 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.259A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 498 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.700A pdb=" N LYS C 57 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 148 removed outlier: 3.785A pdb=" N SER C 148 " --> pdb=" O LYS C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.910A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 removed outlier: 3.535A pdb=" N LEU C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 276 removed outlier: 3.525A pdb=" N VAL C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TRP C 271 " --> pdb=" O LEU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 286 removed outlier: 3.746A pdb=" N VAL C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.632A pdb=" N LEU C 293 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N SER C 295 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'C' and resid 409 through 414 removed outlier: 3.538A pdb=" N LYS C 413 " --> pdb=" O PRO C 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 42 through 58 removed outlier: 4.232A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.736A pdb=" N LYS E 73 " --> pdb=" O LYS E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 111 through 120 Processing helix chain 'E' and resid 134 through 137 removed outlier: 4.139A pdb=" N GLU E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 138 through 148 removed outlier: 3.624A pdb=" N CYS E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 53 removed outlier: 3.713A pdb=" N ARG F 45 " --> pdb=" O TYR F 41 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 52 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 removed outlier: 4.096A pdb=" N LYS G 57 " --> pdb=" O LEU G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 114 removed outlier: 3.660A pdb=" N ALA G 107 " --> pdb=" O HIS G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 142 through 148 removed outlier: 3.735A pdb=" N SER G 148 " --> pdb=" O LYS G 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 4.085A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 176 " --> pdb=" O ALA G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 237 Processing helix chain 'G' and resid 263 through 276 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 288 through 292 removed outlier: 3.702A pdb=" N LYS G 291 " --> pdb=" O PRO G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 312 removed outlier: 4.360A pdb=" N ASN G 307 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 385 through 395 Processing helix chain 'H' and resid 148 through 151 removed outlier: 3.809A pdb=" N LEU H 151 " --> pdb=" O PRO H 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 148 through 151' Processing helix chain 'I' and resid 20 through 30 Processing helix chain 'I' and resid 40 through 56 removed outlier: 4.128A pdb=" N LYS I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 74 removed outlier: 3.788A pdb=" N LYS I 73 " --> pdb=" O LYS I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 101 Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.502A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY I 119 " --> pdb=" O GLY I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 147 removed outlier: 3.999A pdb=" N GLU I 141 " --> pdb=" O GLU I 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 53 removed outlier: 3.911A pdb=" N ILE J 46 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR J 47 " --> pdb=" O ARG J 43 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 155 through 160 removed outlier: 3.513A pdb=" N ARG B 155 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU B 516 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLY B 159 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 514 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 466 " --> pdb=" O ALA B 479 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 173 through 177 removed outlier: 3.582A pdb=" N ASN B 187 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B 185 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TRP B 177 " --> pdb=" O CYS B 183 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS B 183 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU B 218 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASN B 197 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.140A pdb=" N SER B 248 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR B 229 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 246 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TRP B 231 " --> pdb=" O TYR B 244 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N TYR B 244 " --> pdb=" O TRP B 231 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 254 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER B 267 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE B 256 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 283 through 285 removed outlier: 3.646A pdb=" N CYS B 284 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE B 293 " --> pdb=" O CYS B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 328 through 333 removed outlier: 3.521A pdb=" N LEU B 351 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 361 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 373 removed outlier: 6.711A pdb=" N GLY B 385 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU B 373 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N PHE B 383 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 384 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 393 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ALA B 386 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N GLU B 391 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TRP B 405 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 419 through 421 removed outlier: 3.565A pdb=" N VAL B 429 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 455 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP B 441 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.581A pdb=" N TYR C 323 " --> pdb=" O ASN C 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 331 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C 368 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE C 347 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 366 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA C 364 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 315 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 95 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C 244 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ARG C 158 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU C 246 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 156 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG C 248 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL C 154 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 250 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 155 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 214 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 119 through 120 removed outlier: 3.587A pdb=" N CYS C 131 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG C 250 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE C 133 " --> pdb=" O ARG C 250 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET C 254 " --> pdb=" O SER C 251 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 71 through 80 removed outlier: 5.767A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 85 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY D 111 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 94 through 96 removed outlier: 3.881A pdb=" N VAL D 95 " --> pdb=" O LEU D 152 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 152 " --> pdb=" O VAL D 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.517A pdb=" N VAL E 129 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 78 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET E 79 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ILE E 108 " --> pdb=" O MET E 79 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU E 81 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 13 through 16 removed outlier: 3.611A pdb=" N VAL F 14 " --> pdb=" O TYR F 6 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR F 5 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS F 28 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 63 through 64 removed outlier: 3.559A pdb=" N TYR G 323 " --> pdb=" O ASN G 63 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 119 through 120 removed outlier: 3.733A pdb=" N GLY G 119 " --> pdb=" O CYS G 135 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 132 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU G 94 " --> pdb=" O LEU G 132 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL G 261 " --> pdb=" O PHE G 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN G 93 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 178 through 182 removed outlier: 3.828A pdb=" N ARG G 197 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 201 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU G 152 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL G 249 " --> pdb=" O GLU G 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 245 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG G 158 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N MET G 243 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET G 254 " --> pdb=" O SER G 251 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 298 through 300 removed outlier: 5.841A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN G 331 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS G 344 " --> pdb=" O VAL G 335 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG G 368 " --> pdb=" O MET G 345 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE G 347 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE G 366 " --> pdb=" O ILE G 347 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 71 through 80 removed outlier: 5.278A pdb=" N PHE H 76 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LYS H 87 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY H 111 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 61 removed outlier: 3.891A pdb=" N ILE I 78 " --> pdb=" O VAL I 129 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 13 through 16 removed outlier: 3.629A pdb=" N VAL J 14 " --> pdb=" O TYR J 6 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 4 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS J 28 " --> pdb=" O TYR J 5 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1071 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 42 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 7.37 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: 4860 1.34 - 1.46: 3643 1.46 - 1.57: 8636 1.57 - 1.69: 289 1.69 - 1.81: 125 Bond restraints: 17553 Sorted by residual: bond pdb=" C LEU H 158 " pdb=" N PRO H 159 " ideal model delta sigma weight residual 1.334 1.354 -0.020 1.11e-02 8.12e+03 3.33e+00 bond pdb=" CA TYR E 91 " pdb=" CB TYR E 91 " ideal model delta sigma weight residual 1.528 1.568 -0.039 2.61e-02 1.47e+03 2.27e+00 bond pdb=" C GLY B 444 " pdb=" N PRO B 445 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.36e-02 5.41e+03 1.79e+00 bond pdb=" N LEU G 54 " pdb=" CA LEU G 54 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.70e+00 bond pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 1.459 1.474 -0.015 1.16e-02 7.43e+03 1.65e+00 ... (remaining 17548 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 1362 106.87 - 113.65: 9799 113.65 - 120.43: 6430 120.43 - 127.20: 6403 127.20 - 133.98: 464 Bond angle restraints: 24458 Sorted by residual: angle pdb=" CA ASP D 91 " pdb=" C ASP D 91 " pdb=" N GLU D 92 " ideal model delta sigma weight residual 118.81 113.40 5.41 1.15e+00 7.56e-01 2.21e+01 angle pdb=" N VAL C 239 " pdb=" CA VAL C 239 " pdb=" C VAL C 239 " ideal model delta sigma weight residual 113.71 109.66 4.05 9.50e-01 1.11e+00 1.82e+01 angle pdb=" N VAL G 239 " pdb=" CA VAL G 239 " pdb=" C VAL G 239 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 angle pdb=" C PRO C 53 " pdb=" N LEU C 54 " pdb=" CA LEU C 54 " ideal model delta sigma weight residual 120.79 126.37 -5.58 1.39e+00 5.18e-01 1.61e+01 angle pdb=" N VAL C 363 " pdb=" CA VAL C 363 " pdb=" C VAL C 363 " ideal model delta sigma weight residual 113.53 109.70 3.83 9.80e-01 1.04e+00 1.53e+01 ... (remaining 24453 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.19: 10279 34.19 - 68.38: 550 68.38 - 102.57: 77 102.57 - 136.76: 1 136.76 - 170.96: 6 Dihedral angle restraints: 10913 sinusoidal: 5927 harmonic: 4986 Sorted by residual: dihedral pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " pdb=" C1' C R 398 " ideal model delta sinusoidal sigma weight residual -35.00 33.12 -68.12 1 8.00e+00 1.56e-02 9.41e+01 dihedral pdb=" C5' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" O3' C R 398 " ideal model delta sinusoidal sigma weight residual 147.00 81.29 65.71 1 8.00e+00 1.56e-02 8.83e+01 dihedral pdb=" O4' C R 398 " pdb=" C4' C R 398 " pdb=" C3' C R 398 " pdb=" C2' C R 398 " ideal model delta sinusoidal sigma weight residual 24.00 -34.36 58.36 1 8.00e+00 1.56e-02 7.13e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2519 0.055 - 0.111: 262 0.111 - 0.166: 23 0.166 - 0.222: 0 0.222 - 0.277: 2 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C3' C R 398 " pdb=" C4' C R 398 " pdb=" O3' C R 398 " pdb=" C2' C R 398 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C2' C R 398 " pdb=" C3' C R 398 " pdb=" O2' C R 398 " pdb=" C1' C R 398 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" P C R 394 " pdb=" OP1 C R 394 " pdb=" OP2 C R 394 " pdb=" O5' C R 394 " both_signs ideal model delta sigma weight residual True 2.41 -2.56 -0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 2803 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 158 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 159 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP G 52 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO G 53 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 500 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 501 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 501 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 501 " 0.021 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3643 2.79 - 3.32: 13897 3.32 - 3.84: 26781 3.84 - 4.37: 30435 4.37 - 4.90: 51103 Nonbonded interactions: 125859 Sorted by model distance: nonbonded pdb=" O LYS G 291 " pdb=" OG1 THR G 294 " model vdw 2.260 2.440 nonbonded pdb=" OD2 ASP B 422 " pdb=" OG1 THR B 424 " model vdw 2.285 2.440 nonbonded pdb=" O GLY C 383 " pdb=" OG SER C 387 " model vdw 2.290 2.440 nonbonded pdb=" OD1 ASP B 180 " pdb=" OG SER B 182 " model vdw 2.292 2.440 nonbonded pdb=" O ASP G 85 " pdb=" OG1 THR G 89 " model vdw 2.295 2.440 ... (remaining 125854 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 'C' and resid 47 through 395) selection = chain 'G' } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 22 through 150) } ncs_group { reference = chain 'F' selection = (chain 'J' and resid 1 through 62) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.210 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 50.040 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5619 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 : 0.002 0.039 17553 Z= 0.133 Angle : 0.579 6.823 24458 Z= 0.353 Chirality : 0.035 0.277 2806 Planarity : 0.004 0.041 2586 Dihedral : 18.983 170.955 7713 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.16), residues: 1705 helix: -1.49 (0.23), residues: 379 sheet: -2.27 (0.27), residues: 301 loop : -3.49 (0.14), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.002 0.000 HIS H 78 PHE 0.009 0.001 PHE B 419 TYR 0.008 0.001 TYR E 91 ARG 0.002 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 LYS cc_start: 0.8330 (mptt) cc_final: 0.8024 (mmtm) REVERT: D 146 ILE cc_start: 0.7064 (tt) cc_final: 0.6297 (tt) REVERT: G 133 ILE cc_start: 0.5893 (mm) cc_final: 0.5673 (mm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4298 time to fit residues: 184.7375 Evaluate side-chains 140 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 10.0000 chunk 137 optimal weight: 0.4980 chunk 76 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 HIS C 147 GLN C 160 HIS C 244 GLN C 276 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** G 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN G 307 ASN G 331 GLN H 64 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 32 ASN I 68 GLN J 59 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17553 Z= 0.291 Angle : 0.686 8.381 24458 Z= 0.344 Chirality : 0.041 0.234 2806 Planarity : 0.005 0.097 2586 Dihedral : 20.266 174.240 4258 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.58 % Allowed : 15.24 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.18), residues: 1705 helix: -0.61 (0.25), residues: 377 sheet: -2.05 (0.26), residues: 339 loop : -3.03 (0.16), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 380 HIS 0.006 0.001 HIS E 132 PHE 0.019 0.002 PHE C 181 TYR 0.015 0.002 TYR J 6 ARG 0.011 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 94 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 316 MET cc_start: 0.6083 (mmt) cc_final: 0.5868 (mmm) REVERT: D 133 MET cc_start: 0.5224 (mmm) cc_final: 0.4828 (mmt) REVERT: D 144 PHE cc_start: 0.6379 (m-80) cc_final: 0.6168 (m-80) REVERT: E 79 MET cc_start: 0.5827 (mmp) cc_final: 0.5580 (mmp) REVERT: E 128 MET cc_start: 0.4700 (ttp) cc_final: 0.4372 (ttp) REVERT: G 207 TYR cc_start: 0.7113 (t80) cc_final: 0.6840 (t80) REVERT: G 227 ARG cc_start: 0.6409 (ttt180) cc_final: 0.6003 (ttm-80) REVERT: G 371 MET cc_start: 0.5075 (mmm) cc_final: 0.4824 (mtt) outliers start: 39 outliers final: 27 residues processed: 182 average time/residue: 0.3373 time to fit residues: 89.0592 Evaluate side-chains 150 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 122 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 204 MET Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 311 TYR Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 61 ARG Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 ASN ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 63 ASN G 160 HIS G 242 GLN ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 GLN J 44 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17553 Z= 0.230 Angle : 0.609 10.791 24458 Z= 0.302 Chirality : 0.039 0.192 2806 Planarity : 0.004 0.033 2586 Dihedral : 20.212 171.519 4258 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.05 % Allowed : 19.62 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.18), residues: 1705 helix: -0.30 (0.26), residues: 384 sheet: -1.73 (0.26), residues: 325 loop : -2.67 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 257 HIS 0.010 0.001 HIS E 132 PHE 0.012 0.001 PHE C 59 TYR 0.013 0.002 TYR H 149 ARG 0.005 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 124 time to evaluate : 1.771 Fit side-chains revert: symmetry clash REVERT: D 133 MET cc_start: 0.5457 (mmm) cc_final: 0.5081 (mmt) REVERT: D 144 PHE cc_start: 0.6540 (m-80) cc_final: 0.6297 (m-80) REVERT: E 99 GLU cc_start: 0.7159 (pp20) cc_final: 0.6639 (mm-30) REVERT: F 53 LYS cc_start: 0.6718 (mmtm) cc_final: 0.6513 (mmtm) REVERT: G 227 ARG cc_start: 0.6343 (ttt180) cc_final: 0.5751 (ttm-80) REVERT: G 254 MET cc_start: 0.5633 (mmm) cc_final: 0.5363 (mmm) REVERT: G 371 MET cc_start: 0.5315 (mmm) cc_final: 0.4865 (mtt) REVERT: H 124 TYR cc_start: 0.7857 (m-80) cc_final: 0.7607 (m-80) outliers start: 46 outliers final: 33 residues processed: 158 average time/residue: 0.3019 time to fit residues: 71.9421 Evaluate side-chains 137 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 174 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 HIS C 270 GLN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS ** D 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 132 HIS ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 276 HIS ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17553 Z= 0.419 Angle : 0.847 11.445 24458 Z= 0.426 Chirality : 0.047 0.185 2806 Planarity : 0.006 0.046 2586 Dihedral : 20.732 169.809 4258 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.50 % Allowed : 20.48 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.18), residues: 1705 helix: -0.95 (0.25), residues: 385 sheet: -1.38 (0.28), residues: 310 loop : -2.75 (0.17), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 257 HIS 0.014 0.002 HIS B 376 PHE 0.027 0.003 PHE C 59 TYR 0.020 0.003 TYR G 311 ARG 0.020 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 114 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 157 LEU cc_start: 0.4972 (OUTLIER) cc_final: 0.4762 (pp) REVERT: B 373 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6337 (tp) REVERT: C 82 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5306 (tp30) REVERT: D 133 MET cc_start: 0.6172 (mmm) cc_final: 0.5523 (mmt) REVERT: D 136 SER cc_start: 0.7507 (m) cc_final: 0.7109 (p) REVERT: E 99 GLU cc_start: 0.7168 (pp20) cc_final: 0.6812 (mm-30) REVERT: E 128 MET cc_start: 0.4609 (ttm) cc_final: 0.4408 (ttp) REVERT: F 5 TYR cc_start: 0.6863 (OUTLIER) cc_final: 0.6201 (p90) REVERT: G 371 MET cc_start: 0.5171 (mmm) cc_final: 0.4771 (mtt) REVERT: H 124 TYR cc_start: 0.8219 (m-80) cc_final: 0.7929 (m-80) REVERT: H 155 GLN cc_start: 0.6619 (mm-40) cc_final: 0.6291 (mm-40) outliers start: 83 outliers final: 50 residues processed: 185 average time/residue: 0.2745 time to fit residues: 77.0647 Evaluate side-chains 153 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 99 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 344 CYS Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 143 VAL Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 333 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 HIS G 259 HIS ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 17553 Z= 0.165 Angle : 0.595 9.095 24458 Z= 0.293 Chirality : 0.039 0.152 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.416 169.884 4258 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.78 % Allowed : 22.93 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.19), residues: 1705 helix: -0.22 (0.26), residues: 387 sheet: -1.15 (0.29), residues: 325 loop : -2.50 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.005 0.001 HIS H 78 PHE 0.010 0.001 PHE C 91 TYR 0.013 0.001 TYR E 139 ARG 0.006 0.000 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 115 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 226 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.6686 (mp) REVERT: B 373 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6008 (tp) REVERT: C 243 MET cc_start: 0.6682 (tpp) cc_final: 0.6273 (tpt) REVERT: D 133 MET cc_start: 0.5764 (mmm) cc_final: 0.5201 (mmt) REVERT: F 5 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5942 (p90) REVERT: G 371 MET cc_start: 0.5287 (mmm) cc_final: 0.4970 (mtt) REVERT: H 124 TYR cc_start: 0.7974 (m-80) cc_final: 0.7624 (m-80) REVERT: H 155 GLN cc_start: 0.6710 (mm-40) cc_final: 0.6449 (mm-40) outliers start: 57 outliers final: 34 residues processed: 162 average time/residue: 0.2883 time to fit residues: 70.3648 Evaluate side-chains 138 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 101 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 19 LYS Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 102 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN G 259 HIS ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17553 Z= 0.141 Angle : 0.565 8.871 24458 Z= 0.275 Chirality : 0.038 0.156 2806 Planarity : 0.004 0.047 2586 Dihedral : 20.231 172.191 4258 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.72 % Allowed : 23.59 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.19), residues: 1705 helix: 0.15 (0.27), residues: 389 sheet: -0.95 (0.29), residues: 315 loop : -2.30 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.005 0.001 HIS B 366 PHE 0.009 0.001 PHE D 49 TYR 0.014 0.001 TYR B 271 ARG 0.006 0.000 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 110 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.5627 (mmm) cc_final: 0.5093 (mmt) REVERT: E 99 GLU cc_start: 0.7381 (pp20) cc_final: 0.6829 (mm-30) REVERT: F 5 TYR cc_start: 0.6500 (OUTLIER) cc_final: 0.6127 (p90) REVERT: G 371 MET cc_start: 0.5237 (mmm) cc_final: 0.4890 (mtt) REVERT: H 124 TYR cc_start: 0.7818 (m-80) cc_final: 0.7560 (m-80) outliers start: 41 outliers final: 30 residues processed: 146 average time/residue: 0.2865 time to fit residues: 63.7993 Evaluate side-chains 126 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 30.0000 chunk 19 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 GLN ** E 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17553 Z= 0.318 Angle : 0.736 13.337 24458 Z= 0.364 Chirality : 0.043 0.205 2806 Planarity : 0.005 0.048 2586 Dihedral : 20.545 168.738 4258 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.04 % Allowed : 23.46 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.19), residues: 1705 helix: -0.50 (0.25), residues: 393 sheet: -1.12 (0.29), residues: 316 loop : -2.41 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 380 HIS 0.010 0.002 HIS B 376 PHE 0.021 0.002 PHE C 59 TYR 0.015 0.002 TYR G 86 ARG 0.007 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 101 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 260 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7910 (mmt) REVERT: D 133 MET cc_start: 0.6053 (mmm) cc_final: 0.5230 (mmt) REVERT: E 99 GLU cc_start: 0.7172 (pp20) cc_final: 0.6703 (mm-30) REVERT: F 5 TYR cc_start: 0.6724 (OUTLIER) cc_final: 0.5965 (p90) REVERT: G 371 MET cc_start: 0.5266 (mmm) cc_final: 0.4893 (mtt) outliers start: 61 outliers final: 51 residues processed: 149 average time/residue: 0.2630 time to fit residues: 61.2515 Evaluate side-chains 148 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 95 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain C residue 260 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 140 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 137 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN G 259 HIS ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17553 Z= 0.176 Angle : 0.602 13.348 24458 Z= 0.293 Chirality : 0.039 0.154 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.457 170.280 4258 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.51 % Allowed : 24.65 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.19), residues: 1705 helix: -0.08 (0.27), residues: 390 sheet: -1.03 (0.29), residues: 311 loop : -2.28 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 517 HIS 0.014 0.001 HIS B 366 PHE 0.023 0.001 PHE H 123 TYR 0.011 0.001 TYR E 139 ARG 0.003 0.000 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 96 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ILE cc_start: 0.7306 (mm) cc_final: 0.7033 (mp) REVERT: D 133 MET cc_start: 0.5958 (mmm) cc_final: 0.5239 (mmt) REVERT: F 5 TYR cc_start: 0.6449 (OUTLIER) cc_final: 0.5815 (p90) REVERT: G 371 MET cc_start: 0.5080 (mmm) cc_final: 0.4767 (mtt) REVERT: H 155 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6335 (mm-40) outliers start: 53 outliers final: 46 residues processed: 138 average time/residue: 0.2641 time to fit residues: 57.7954 Evaluate side-chains 142 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 95 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 31 GLN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 169 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 30.0000 chunk 152 optimal weight: 0.8980 chunk 162 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 171 optimal weight: 10.0000 overall best weight: 2.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17553 Z= 0.210 Angle : 0.625 13.736 24458 Z= 0.304 Chirality : 0.040 0.186 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.508 169.862 4258 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 3.58 % Allowed : 24.72 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.19), residues: 1705 helix: -0.13 (0.26), residues: 394 sheet: -1.07 (0.30), residues: 305 loop : -2.22 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 380 HIS 0.014 0.001 HIS B 366 PHE 0.024 0.001 PHE H 123 TYR 0.011 0.001 TYR H 145 ARG 0.004 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5639 (OUTLIER) cc_final: 0.5198 (tt0) REVERT: D 133 MET cc_start: 0.6009 (mmm) cc_final: 0.5257 (mmt) REVERT: E 79 MET cc_start: 0.6806 (ptp) cc_final: 0.6581 (ptp) REVERT: E 99 GLU cc_start: 0.7009 (pp20) cc_final: 0.6679 (mm-30) REVERT: F 5 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.5927 (p90) REVERT: G 371 MET cc_start: 0.5180 (mmm) cc_final: 0.4870 (mtt) REVERT: H 155 GLN cc_start: 0.6603 (mm-40) cc_final: 0.6238 (mm-40) REVERT: J 23 MET cc_start: 0.4537 (tpp) cc_final: 0.4269 (tpp) outliers start: 54 outliers final: 46 residues processed: 139 average time/residue: 0.2622 time to fit residues: 57.6661 Evaluate side-chains 143 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 95 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17553 Z= 0.192 Angle : 0.614 10.978 24458 Z= 0.299 Chirality : 0.039 0.186 2806 Planarity : 0.004 0.042 2586 Dihedral : 20.517 170.789 4258 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.25 % Allowed : 25.05 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.20), residues: 1705 helix: -0.03 (0.27), residues: 389 sheet: -0.91 (0.30), residues: 295 loop : -2.17 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 380 HIS 0.011 0.001 HIS B 366 PHE 0.022 0.001 PHE H 123 TYR 0.010 0.001 TYR E 139 ARG 0.003 0.000 ARG B 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3410 Ramachandran restraints generated. 1705 Oldfield, 0 Emsley, 1705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 104 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 133 MET cc_start: 0.5902 (mmm) cc_final: 0.5188 (mmt) REVERT: E 79 MET cc_start: 0.6812 (ptp) cc_final: 0.6461 (ptp) REVERT: E 99 GLU cc_start: 0.7074 (pp20) cc_final: 0.6870 (mm-30) REVERT: F 5 TYR cc_start: 0.6583 (OUTLIER) cc_final: 0.5819 (p90) REVERT: G 133 ILE cc_start: 0.6206 (mm) cc_final: 0.5797 (mt) REVERT: G 371 MET cc_start: 0.5336 (mmm) cc_final: 0.5080 (mtt) REVERT: H 155 GLN cc_start: 0.6573 (mm-40) cc_final: 0.6171 (mm-40) REVERT: J 23 MET cc_start: 0.4672 (tpp) cc_final: 0.4430 (tpp) outliers start: 49 outliers final: 47 residues processed: 141 average time/residue: 0.2539 time to fit residues: 56.5932 Evaluate side-chains 145 residues out of total 1509 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 97 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 323 TYR Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 408 THR Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 76 PHE Chi-restraints excluded: chain D residue 92 GLU Chi-restraints excluded: chain D residue 106 ASN Chi-restraints excluded: chain E residue 48 TYR Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain F residue 5 TYR Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 219 SER Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 344 CYS Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 132 ASN Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain J residue 2 PHE Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** H 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.103472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.084358 restraints weight = 67240.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.084307 restraints weight = 67501.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.084823 restraints weight = 63018.065| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.7398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17553 Z= 0.166 Angle : 0.601 11.563 24458 Z= 0.288 Chirality : 0.039 0.228 2806 Planarity : 0.004 0.043 2586 Dihedral : 20.476 171.560 4258 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.18 % Allowed : 25.12 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.20), residues: 1705 helix: 0.02 (0.27), residues: 389 sheet: -0.78 (0.31), residues: 280 loop : -2.13 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 257 HIS 0.006 0.001 HIS B 366 PHE 0.020 0.001 PHE H 123 TYR 0.013 0.001 TYR B 271 ARG 0.004 0.000 ARG B 513 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2935.50 seconds wall clock time: 54 minutes 23.59 seconds (3263.59 seconds total)