Starting phenix.real_space_refine on Mon Mar 11 05:59:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/03_2024/6jnf_9851_updated.pdb" } resolution = 3.81 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= 0.012 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 1 5.49 5 S 20 5.16 5 C 4681 2.51 5 N 1215 2.21 5 O 1354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 345": "OD1" <-> "OD2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 170": "OD1" <-> "OD2" Residue "F PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 242": "OD1" <-> "OD2" Residue "F PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 345": "OD1" <-> "OD2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "I TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 55": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7271 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2363 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 4 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 336 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "C" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 342 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 292 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "F" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2363 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 4 Chain: "G" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 336 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "H" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 342 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 292 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 281 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'46E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.52, per 1000 atoms: 0.62 Number of scatterers: 7271 At special positions: 0 Unit cell: (138.19, 114.943, 94.2795, 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 20 16.00 P 1 15.00 O 1354 8.00 N 1215 7.00 C 4681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 8 sheets defined 22.5% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.754A pdb=" N GLN A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 372' Processing helix chain 'B' and resid 18 through 25 removed outlier: 3.575A pdb=" N LEU B 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 24 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 42 removed outlier: 3.571A pdb=" N LEU B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.745A pdb=" N THR C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 129 removed outlier: 3.710A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 3.893A pdb=" N THR D 24 " --> pdb=" O GLN D 20 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR D 30 " --> pdb=" O LYS D 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D 31 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP D 36 " --> pdb=" O ALA D 32 " (cutoff:3.500A) Proline residue: D 39 - end of helix Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'E' and resid 31 through 49 removed outlier: 3.726A pdb=" N THR E 34 " --> pdb=" O PRO E 31 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE E 35 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA E 36 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN E 38 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY E 39 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE E 42 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E 43 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA E 44 " --> pdb=" O PHE E 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 47 " --> pdb=" O ALA E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 56 removed outlier: 3.508A pdb=" N MET E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 56' Processing helix chain 'F' and resid 68 through 71 No H-bonds generated for 'chain 'F' and resid 68 through 71' Processing helix chain 'F' and resid 368 through 372 removed outlier: 3.752A pdb=" N GLN F 371 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN F 372 " --> pdb=" O MET F 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 368 through 372' Processing helix chain 'G' and resid 18 through 25 removed outlier: 3.576A pdb=" N LEU G 23 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR G 24 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 42 removed outlier: 3.572A pdb=" N LEU G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 38 " --> pdb=" O PRO G 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA G 42 " --> pdb=" O TYR G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'H' and resid 97 through 101 removed outlier: 3.745A pdb=" N THR H 101 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.709A pdb=" N LEU H 118 " --> pdb=" O SER H 114 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU H 120 " --> pdb=" O SER H 116 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU H 123 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU H 125 " --> pdb=" O GLN H 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 3.893A pdb=" N THR I 24 " --> pdb=" O GLN I 20 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU I 25 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA I 29 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR I 30 " --> pdb=" O LYS I 26 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL I 31 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE I 34 " --> pdb=" O TYR I 30 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP I 36 " --> pdb=" O ALA I 32 " (cutoff:3.500A) Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 45 through 48 No H-bonds generated for 'chain 'I' and resid 45 through 48' Processing helix chain 'J' and resid 31 through 49 removed outlier: 3.727A pdb=" N THR J 34 " --> pdb=" O PRO J 31 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE J 35 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA J 36 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASN J 38 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY J 39 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE J 42 " --> pdb=" O GLY J 39 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL J 43 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA J 44 " --> pdb=" O PHE J 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J 46 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA J 47 " --> pdb=" O ALA J 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.508A pdb=" N MET J 56 " --> pdb=" O PRO J 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 52 through 56' Processing sheet with id= A, first strand: chain 'A' and resid 306 through 309 removed outlier: 4.148A pdb=" N SER A 312 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 344 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 342 " --> pdb=" O CYS A 326 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 338 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 356 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 85 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A 87 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 91 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 84 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 104 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 121 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 99 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 119 " --> pdb=" O GLN A 99 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 115 through 117 removed outlier: 3.616A pdb=" N ILE A 131 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 137 through 141 removed outlier: 3.512A pdb=" N VAL A 137 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 139 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 153 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 201 through 203 removed outlier: 4.097A pdb=" N GLN A 203 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 234 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 258 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 256 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 257 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 259 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE A 271 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 274 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER A 300 " --> pdb=" O THR A 274 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 306 through 309 removed outlier: 4.150A pdb=" N SER F 312 " --> pdb=" O TYR F 309 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE F 344 " --> pdb=" O VAL F 324 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 342 " --> pdb=" O CYS F 326 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 338 " --> pdb=" O ARG F 330 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY F 356 " --> pdb=" O LEU F 339 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 85 " --> pdb=" O CYS F 355 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 87 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA F 91 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 84 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE F 104 " --> pdb=" O ALA F 86 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA F 121 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN F 99 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU F 119 " --> pdb=" O GLN F 99 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 115 through 117 removed outlier: 3.616A pdb=" N ILE F 131 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.512A pdb=" N VAL F 137 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY F 139 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL F 153 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 201 through 203 removed outlier: 4.097A pdb=" N GLN F 203 " --> pdb=" O LEU F 211 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR F 234 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER F 258 " --> pdb=" O SER F 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE F 256 " --> pdb=" O GLN F 248 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA F 257 " --> pdb=" O THR F 273 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU F 259 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE F 271 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR F 274 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER F 300 " --> pdb=" O THR F 274 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.79 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1185 1.30 - 1.43: 1964 1.43 - 1.55: 4237 1.55 - 1.68: 4 1.68 - 1.80: 32 Bond restraints: 7422 Sorted by residual: bond pdb=" C21 46E A 401 " pdb=" O21 46E A 401 " ideal model delta sigma weight residual 1.331 1.402 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C31 46E A 401 " pdb=" O31 46E A 401 " ideal model delta sigma weight residual 1.327 1.396 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C SER B 55 " pdb=" N PRO B 56 " ideal model delta sigma weight residual 1.334 1.400 -0.066 2.34e-02 1.83e+03 7.94e+00 bond pdb=" C SER G 55 " pdb=" N PRO G 56 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.34e-02 1.83e+03 7.81e+00 bond pdb=" C GLN F 294 " pdb=" N PRO F 295 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.19e+00 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.34: 195 106.34 - 113.65: 4073 113.65 - 120.96: 3582 120.96 - 128.28: 2125 128.28 - 135.59: 78 Bond angle restraints: 10053 Sorted by residual: angle pdb=" N ILE A 293 " pdb=" CA ILE A 293 " pdb=" C ILE A 293 " ideal model delta sigma weight residual 113.20 106.10 7.10 9.60e-01 1.09e+00 5.46e+01 angle pdb=" N ILE F 293 " pdb=" CA ILE F 293 " pdb=" C ILE F 293 " ideal model delta sigma weight residual 113.20 106.10 7.10 9.60e-01 1.09e+00 5.46e+01 angle pdb=" O11 46E A 401 " pdb=" P 46E A 401 " pdb=" O13 46E A 401 " ideal model delta sigma weight residual 93.37 111.27 -17.90 3.00e+00 1.11e-01 3.56e+01 angle pdb=" C VAL A 205 " pdb=" N THR A 206 " pdb=" CA THR A 206 " ideal model delta sigma weight residual 121.80 135.59 -13.79 2.44e+00 1.68e-01 3.19e+01 angle pdb=" C VAL F 205 " pdb=" N THR F 206 " pdb=" CA THR F 206 " ideal model delta sigma weight residual 121.80 135.50 -13.70 2.44e+00 1.68e-01 3.15e+01 ... (remaining 10048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3738 17.79 - 35.59: 503 35.59 - 53.38: 90 53.38 - 71.17: 25 71.17 - 88.97: 17 Dihedral angle restraints: 4373 sinusoidal: 1719 harmonic: 2654 Sorted by residual: dihedral pdb=" CA VAL A 205 " pdb=" C VAL A 205 " pdb=" N THR A 206 " pdb=" CA THR A 206 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA VAL F 205 " pdb=" C VAL F 205 " pdb=" N THR F 206 " pdb=" CA THR F 206 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ARG B 47 " pdb=" C ARG B 47 " pdb=" N PRO B 48 " pdb=" CA PRO B 48 " ideal model delta harmonic sigma weight residual -180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 4370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 822 0.060 - 0.120: 235 0.120 - 0.180: 71 0.180 - 0.241: 9 0.241 - 0.301: 4 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CB VAL F 332 " pdb=" CA VAL F 332 " pdb=" CG1 VAL F 332 " pdb=" CG2 VAL F 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB VAL A 332 " pdb=" CA VAL A 332 " pdb=" CG1 VAL A 332 " pdb=" CG2 VAL A 332 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ASN F 321 " pdb=" N ASN F 321 " pdb=" C ASN F 321 " pdb=" CB ASN F 321 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1138 not shown) Planarity restraints: 1272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 333 " -0.048 5.00e-02 4.00e+02 7.24e-02 8.40e+00 pdb=" N PRO A 334 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 333 " 0.048 5.00e-02 4.00e+02 7.20e-02 8.29e+00 pdb=" N PRO F 334 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO F 334 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 334 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.39e+00 pdb=" N PRO A 207 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " 0.038 5.00e-02 4.00e+02 ... (remaining 1269 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2420 2.82 - 3.34: 6052 3.34 - 3.86: 10515 3.86 - 4.38: 11344 4.38 - 4.90: 20365 Nonbonded interactions: 50696 Sorted by model distance: nonbonded pdb=" NE2 GLN F 203 " pdb=" O ILE I 41 " model vdw 2.304 2.520 nonbonded pdb=" O PHE J 27 " pdb=" OG SER J 30 " model vdw 2.306 2.440 nonbonded pdb=" O PHE E 27 " pdb=" OG SER E 30 " model vdw 2.306 2.440 nonbonded pdb=" OG SER A 246 " pdb=" N GLY A 247 " model vdw 2.334 2.520 nonbonded pdb=" OG SER F 246 " pdb=" N GLY F 247 " model vdw 2.335 2.520 ... (remaining 50691 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 47 through 373) selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 1.910 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.790 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.009 0.071 7422 Z= 0.551 Angle : 1.227 17.959 10053 Z= 0.617 Chirality : 0.063 0.301 1141 Planarity : 0.007 0.072 1272 Dihedral : 17.480 88.966 2653 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 1.02 % Allowed : 18.41 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.16 (0.22), residues: 888 helix: -4.57 (0.14), residues: 202 sheet: -3.78 (0.22), residues: 366 loop : -3.66 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 36 HIS 0.007 0.001 HIS I 43 PHE 0.030 0.003 PHE A 92 TYR 0.024 0.002 TYR F 143 ARG 0.003 0.001 ARG F 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLN cc_start: 0.8420 (pp30) cc_final: 0.7844 (pp30) REVERT: A 217 TYR cc_start: 0.8576 (t80) cc_final: 0.8194 (t80) REVERT: A 219 ARG cc_start: 0.8833 (ttt180) cc_final: 0.8501 (ttp-170) REVERT: B 26 ASN cc_start: 0.7181 (t0) cc_final: 0.6845 (t0) REVERT: C 87 PHE cc_start: 0.6500 (p90) cc_final: 0.6296 (p90) REVERT: C 94 LYS cc_start: 0.9047 (tptt) cc_final: 0.8429 (tppt) REVERT: D 42 TRP cc_start: 0.8507 (t60) cc_final: 0.7847 (t-100) REVERT: E 41 PHE cc_start: 0.9204 (m-80) cc_final: 0.8979 (m-80) REVERT: F 203 GLN cc_start: 0.8300 (pp30) cc_final: 0.7892 (pp30) REVERT: F 214 GLU cc_start: 0.8795 (pp20) cc_final: 0.8585 (pp20) REVERT: F 219 ARG cc_start: 0.8803 (ttt180) cc_final: 0.8572 (ttp-170) REVERT: J 41 PHE cc_start: 0.9164 (m-80) cc_final: 0.8887 (m-80) outliers start: 8 outliers final: 4 residues processed: 202 average time/residue: 0.2032 time to fit residues: 53.5128 Evaluate side-chains 161 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.0870 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN F 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7422 Z= 0.174 Angle : 0.756 11.971 10053 Z= 0.367 Chirality : 0.044 0.158 1141 Planarity : 0.005 0.055 1272 Dihedral : 8.341 61.627 1003 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 1.41 % Allowed : 26.09 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.25), residues: 888 helix: -3.41 (0.24), residues: 206 sheet: -2.98 (0.25), residues: 366 loop : -3.25 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 36 HIS 0.001 0.000 HIS B 43 PHE 0.009 0.001 PHE A 92 TYR 0.011 0.001 TYR I 30 ARG 0.003 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 0.834 Fit side-chains REVERT: A 87 ASP cc_start: 0.8307 (p0) cc_final: 0.8027 (p0) REVERT: A 164 MET cc_start: 0.8016 (mpp) cc_final: 0.7669 (mmm) REVERT: A 167 LEU cc_start: 0.8601 (tt) cc_final: 0.7663 (mp) REVERT: A 203 GLN cc_start: 0.7883 (pp30) cc_final: 0.7625 (pp30) REVERT: A 217 TYR cc_start: 0.8402 (t80) cc_final: 0.8068 (t80) REVERT: A 219 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8375 (ttp-170) REVERT: A 367 LEU cc_start: 0.8310 (tp) cc_final: 0.8065 (tp) REVERT: A 369 MET cc_start: 0.8819 (ttm) cc_final: 0.8486 (ttp) REVERT: C 87 PHE cc_start: 0.6663 (p90) cc_final: 0.6339 (p90) REVERT: C 94 LYS cc_start: 0.9001 (tptt) cc_final: 0.8493 (tppt) REVERT: D 42 TRP cc_start: 0.8790 (t60) cc_final: 0.7537 (t60) REVERT: E 41 PHE cc_start: 0.9193 (m-80) cc_final: 0.8949 (m-80) REVERT: F 87 ASP cc_start: 0.8320 (p0) cc_final: 0.8041 (p0) REVERT: F 164 MET cc_start: 0.8050 (mpp) cc_final: 0.7786 (mmm) REVERT: F 167 LEU cc_start: 0.8628 (tt) cc_final: 0.7707 (mp) REVERT: F 214 GLU cc_start: 0.8701 (pp20) cc_final: 0.8497 (pp20) REVERT: F 365 GLN cc_start: 0.7883 (pm20) cc_final: 0.7659 (pm20) REVERT: F 367 LEU cc_start: 0.8291 (tp) cc_final: 0.8078 (tp) REVERT: J 41 PHE cc_start: 0.9152 (m-80) cc_final: 0.8859 (m-80) outliers start: 11 outliers final: 11 residues processed: 178 average time/residue: 0.1988 time to fit residues: 46.7904 Evaluate side-chains 176 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain I residue 17 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 30.0000 chunk 24 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7422 Z= 0.309 Angle : 0.808 12.376 10053 Z= 0.392 Chirality : 0.047 0.167 1141 Planarity : 0.005 0.048 1272 Dihedral : 8.164 68.585 1001 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 5.24 % Allowed : 26.34 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.27), residues: 888 helix: -2.29 (0.32), residues: 198 sheet: -2.79 (0.26), residues: 368 loop : -2.80 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 100 HIS 0.002 0.001 HIS G 43 PHE 0.018 0.002 PHE F 92 TYR 0.013 0.002 TYR A 79 ARG 0.002 0.000 ARG A 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 164 MET cc_start: 0.8018 (mpp) cc_final: 0.7665 (mmm) REVERT: A 203 GLN cc_start: 0.7995 (pp30) cc_final: 0.7633 (pp30) REVERT: A 217 TYR cc_start: 0.8428 (t80) cc_final: 0.8171 (t80) REVERT: A 219 ARG cc_start: 0.8745 (ttt180) cc_final: 0.8436 (ttt180) REVERT: A 369 MET cc_start: 0.8807 (ttm) cc_final: 0.8477 (ttt) REVERT: B 35 PHE cc_start: 0.8945 (t80) cc_final: 0.8661 (t80) REVERT: C 87 PHE cc_start: 0.6519 (p90) cc_final: 0.6124 (p90) REVERT: C 94 LYS cc_start: 0.8996 (tptt) cc_final: 0.8498 (tppt) REVERT: D 42 TRP cc_start: 0.8839 (t60) cc_final: 0.7493 (t60) REVERT: E 25 GLN cc_start: 0.7721 (tp-100) cc_final: 0.6819 (mp10) REVERT: E 41 PHE cc_start: 0.9253 (m-80) cc_final: 0.8971 (m-80) REVERT: F 164 MET cc_start: 0.8041 (mpp) cc_final: 0.7765 (mmm) REVERT: F 219 ARG cc_start: 0.8446 (ttt180) cc_final: 0.8080 (ttp-170) REVERT: F 369 MET cc_start: 0.8831 (ttm) cc_final: 0.8463 (ttt) REVERT: G 35 PHE cc_start: 0.8909 (t80) cc_final: 0.8622 (t80) REVERT: I 44 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8621 (mm) REVERT: J 41 PHE cc_start: 0.9178 (m-80) cc_final: 0.8900 (m-80) outliers start: 41 outliers final: 26 residues processed: 196 average time/residue: 0.1769 time to fit residues: 47.0822 Evaluate side-chains 186 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 0.0070 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 85 optimal weight: 0.0970 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN F 311 GLN J 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7422 Z= 0.158 Angle : 0.750 12.253 10053 Z= 0.350 Chirality : 0.044 0.192 1141 Planarity : 0.004 0.053 1272 Dihedral : 6.925 76.414 1001 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.43 % Allowed : 30.69 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.28), residues: 888 helix: -1.85 (0.34), residues: 198 sheet: -2.33 (0.26), residues: 366 loop : -2.61 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 260 HIS 0.001 0.000 HIS A 346 PHE 0.010 0.001 PHE A 359 TYR 0.008 0.001 TYR A 309 ARG 0.002 0.000 ARG F 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.7990 (p0) cc_final: 0.7766 (p0) REVERT: A 164 MET cc_start: 0.7994 (mpp) cc_final: 0.7745 (mmm) REVERT: A 167 LEU cc_start: 0.8548 (tt) cc_final: 0.7733 (mp) REVERT: A 217 TYR cc_start: 0.8277 (t80) cc_final: 0.7882 (t80) REVERT: A 219 ARG cc_start: 0.8691 (ttt180) cc_final: 0.8128 (ttt-90) REVERT: A 367 LEU cc_start: 0.8234 (tp) cc_final: 0.7963 (tp) REVERT: A 369 MET cc_start: 0.8745 (ttm) cc_final: 0.8462 (ttt) REVERT: B 35 PHE cc_start: 0.8860 (t80) cc_final: 0.8529 (t80) REVERT: C 87 PHE cc_start: 0.6506 (p90) cc_final: 0.6258 (p90) REVERT: C 94 LYS cc_start: 0.8964 (tptt) cc_final: 0.8459 (tppt) REVERT: C 122 GLN cc_start: 0.7915 (pt0) cc_final: 0.7494 (tt0) REVERT: D 18 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8645 (tp40) REVERT: D 27 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8579 (tm-30) REVERT: D 42 TRP cc_start: 0.8821 (t60) cc_final: 0.7267 (t60) REVERT: E 25 GLN cc_start: 0.7626 (tp-100) cc_final: 0.6905 (mp10) REVERT: E 41 PHE cc_start: 0.9243 (m-80) cc_final: 0.8958 (m-80) REVERT: F 87 ASP cc_start: 0.7991 (p0) cc_final: 0.7784 (p0) REVERT: F 164 MET cc_start: 0.8016 (mpp) cc_final: 0.7748 (mmm) REVERT: F 167 LEU cc_start: 0.8560 (tt) cc_final: 0.7771 (mp) REVERT: F 241 GLN cc_start: 0.8398 (mm110) cc_final: 0.8180 (mp10) REVERT: F 367 LEU cc_start: 0.8225 (tp) cc_final: 0.7967 (tp) REVERT: F 369 MET cc_start: 0.8771 (ttm) cc_final: 0.8491 (ttt) REVERT: G 35 PHE cc_start: 0.8877 (t80) cc_final: 0.8513 (t80) REVERT: H 122 GLN cc_start: 0.7970 (pt0) cc_final: 0.7539 (tt0) REVERT: J 41 PHE cc_start: 0.9159 (m-80) cc_final: 0.8878 (m-80) outliers start: 19 outliers final: 11 residues processed: 195 average time/residue: 0.1744 time to fit residues: 46.0661 Evaluate side-chains 179 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 168 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7422 Z= 0.314 Angle : 0.792 12.255 10053 Z= 0.384 Chirality : 0.046 0.170 1141 Planarity : 0.004 0.053 1272 Dihedral : 7.373 79.273 999 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 4.73 % Allowed : 30.56 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.29), residues: 888 helix: -1.42 (0.36), residues: 198 sheet: -2.39 (0.26), residues: 368 loop : -2.47 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.002 0.001 HIS G 43 PHE 0.018 0.002 PHE F 92 TYR 0.012 0.001 TYR A 79 ARG 0.003 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 89 ASN cc_start: 0.7649 (OUTLIER) cc_final: 0.7441 (p0) REVERT: A 183 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8358 (mm) REVERT: A 217 TYR cc_start: 0.8390 (t80) cc_final: 0.8080 (t80) REVERT: A 219 ARG cc_start: 0.8701 (ttt180) cc_final: 0.7916 (ttt-90) REVERT: A 367 LEU cc_start: 0.8346 (tp) cc_final: 0.8140 (tp) REVERT: A 369 MET cc_start: 0.8772 (ttm) cc_final: 0.8474 (ttt) REVERT: B 35 PHE cc_start: 0.8928 (t80) cc_final: 0.8452 (t80) REVERT: C 87 PHE cc_start: 0.6486 (p90) cc_final: 0.6279 (p90) REVERT: C 94 LYS cc_start: 0.8987 (tptt) cc_final: 0.8485 (tppt) REVERT: C 122 GLN cc_start: 0.7987 (pt0) cc_final: 0.7614 (tt0) REVERT: D 22 GLU cc_start: 0.8671 (pm20) cc_final: 0.8418 (pm20) REVERT: D 42 TRP cc_start: 0.8838 (t60) cc_final: 0.7293 (t60) REVERT: E 25 GLN cc_start: 0.7643 (tp-100) cc_final: 0.6918 (mp10) REVERT: E 41 PHE cc_start: 0.9273 (m-80) cc_final: 0.8999 (m-80) REVERT: F 89 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7443 (p0) REVERT: F 183 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8471 (mm) REVERT: F 219 ARG cc_start: 0.8481 (ttt-90) cc_final: 0.8122 (ttt-90) REVERT: F 369 MET cc_start: 0.8796 (ttm) cc_final: 0.8487 (ttt) REVERT: G 35 PHE cc_start: 0.8895 (t80) cc_final: 0.8430 (t80) REVERT: H 122 GLN cc_start: 0.7971 (pt0) cc_final: 0.7595 (tt0) REVERT: J 41 PHE cc_start: 0.9180 (m-80) cc_final: 0.8910 (m-80) outliers start: 37 outliers final: 27 residues processed: 191 average time/residue: 0.1688 time to fit residues: 44.8853 Evaluate side-chains 190 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 159 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 89 ASN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 88 VAL Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7422 Z= 0.191 Angle : 0.751 13.991 10053 Z= 0.352 Chirality : 0.044 0.162 1141 Planarity : 0.004 0.057 1272 Dihedral : 6.841 80.470 999 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.26 % Favored : 88.74 % Rotamer: Outliers : 4.22 % Allowed : 31.46 % Favored : 64.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.29), residues: 888 helix: -1.27 (0.37), residues: 198 sheet: -2.14 (0.27), residues: 366 loop : -2.35 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 260 HIS 0.001 0.000 HIS G 43 PHE 0.014 0.001 PHE A 359 TYR 0.017 0.001 TYR F 217 ARG 0.002 0.000 ARG A 315 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 168 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8215 (p0) cc_final: 0.7922 (p0) REVERT: A 167 LEU cc_start: 0.8542 (tt) cc_final: 0.7723 (mp) REVERT: A 217 TYR cc_start: 0.8339 (t80) cc_final: 0.8034 (t80) REVERT: A 219 ARG cc_start: 0.8700 (ttt180) cc_final: 0.8165 (ttt-90) REVERT: A 367 LEU cc_start: 0.8246 (tp) cc_final: 0.8008 (tp) REVERT: A 369 MET cc_start: 0.8701 (ttm) cc_final: 0.8393 (ttt) REVERT: B 35 PHE cc_start: 0.8859 (t80) cc_final: 0.8545 (t80) REVERT: B 52 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7231 (p0) REVERT: C 94 LYS cc_start: 0.8969 (tptt) cc_final: 0.8472 (tppt) REVERT: C 122 GLN cc_start: 0.7896 (pt0) cc_final: 0.7570 (tt0) REVERT: E 25 GLN cc_start: 0.7674 (tp-100) cc_final: 0.7049 (mp10) REVERT: E 41 PHE cc_start: 0.9264 (m-80) cc_final: 0.8991 (m-80) REVERT: F 87 ASP cc_start: 0.8243 (p0) cc_final: 0.7954 (p0) REVERT: F 167 LEU cc_start: 0.8549 (tt) cc_final: 0.7741 (mp) REVERT: F 219 ARG cc_start: 0.8466 (ttt-90) cc_final: 0.7500 (ttt-90) REVERT: F 367 LEU cc_start: 0.8318 (tp) cc_final: 0.8110 (tp) REVERT: F 369 MET cc_start: 0.8721 (ttm) cc_final: 0.8399 (ttt) REVERT: G 35 PHE cc_start: 0.8873 (t80) cc_final: 0.8558 (t80) REVERT: G 52 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7485 (p0) REVERT: H 122 GLN cc_start: 0.7893 (pt0) cc_final: 0.7560 (tt0) REVERT: I 44 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8583 (mm) REVERT: J 41 PHE cc_start: 0.9187 (m-80) cc_final: 0.8921 (m-80) REVERT: J 56 MET cc_start: 0.8586 (tpt) cc_final: 0.8002 (tpt) outliers start: 33 outliers final: 21 residues processed: 195 average time/residue: 0.1635 time to fit residues: 43.9300 Evaluate side-chains 187 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7422 Z= 0.255 Angle : 0.784 13.281 10053 Z= 0.373 Chirality : 0.045 0.169 1141 Planarity : 0.004 0.055 1272 Dihedral : 6.957 79.372 999 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer: Outliers : 5.63 % Allowed : 31.59 % Favored : 62.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.30), residues: 888 helix: -1.08 (0.38), residues: 198 sheet: -2.08 (0.27), residues: 366 loop : -2.31 (0.39), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 260 HIS 0.002 0.000 HIS G 43 PHE 0.016 0.001 PHE A 359 TYR 0.016 0.001 TYR F 217 ARG 0.002 0.000 ARG F 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 168 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8378 (p0) cc_final: 0.8085 (p0) REVERT: A 89 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7356 (p0) REVERT: A 156 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8231 (tt0) REVERT: A 183 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8335 (mm) REVERT: A 217 TYR cc_start: 0.8391 (t80) cc_final: 0.8148 (t80) REVERT: A 219 ARG cc_start: 0.8663 (ttt180) cc_final: 0.8168 (ttt-90) REVERT: A 367 LEU cc_start: 0.8338 (tp) cc_final: 0.8118 (tp) REVERT: A 369 MET cc_start: 0.8701 (ttm) cc_final: 0.8384 (ttt) REVERT: B 35 PHE cc_start: 0.8871 (t80) cc_final: 0.8548 (t80) REVERT: B 52 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7089 (p0) REVERT: C 94 LYS cc_start: 0.8970 (tptt) cc_final: 0.8486 (tppt) REVERT: C 122 GLN cc_start: 0.7862 (pt0) cc_final: 0.7568 (tt0) REVERT: D 18 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8381 (tp40) REVERT: D 22 GLU cc_start: 0.8462 (pm20) cc_final: 0.7705 (pm20) REVERT: D 44 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8518 (mm) REVERT: E 25 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7078 (mp10) REVERT: E 41 PHE cc_start: 0.9291 (m-80) cc_final: 0.9064 (m-80) REVERT: F 87 ASP cc_start: 0.8397 (p0) cc_final: 0.8092 (p0) REVERT: F 156 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: F 183 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8403 (mm) REVERT: F 367 LEU cc_start: 0.8424 (tp) cc_final: 0.8223 (tp) REVERT: F 369 MET cc_start: 0.8719 (ttm) cc_final: 0.8389 (ttt) REVERT: G 35 PHE cc_start: 0.8887 (t80) cc_final: 0.8565 (t80) REVERT: G 52 ASN cc_start: 0.7611 (OUTLIER) cc_final: 0.7227 (p0) REVERT: H 122 GLN cc_start: 0.7898 (pt0) cc_final: 0.7588 (tt0) REVERT: J 41 PHE cc_start: 0.9203 (m-80) cc_final: 0.8941 (m-80) outliers start: 44 outliers final: 34 residues processed: 203 average time/residue: 0.1695 time to fit residues: 46.8786 Evaluate side-chains 205 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 89 ASN Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 156 GLN Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 156 GLN Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7422 Z= 0.179 Angle : 0.786 18.044 10053 Z= 0.364 Chirality : 0.044 0.167 1141 Planarity : 0.004 0.057 1272 Dihedral : 6.463 80.095 999 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer: Outliers : 5.50 % Allowed : 31.33 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.30), residues: 888 helix: -1.13 (0.37), residues: 198 sheet: -1.85 (0.27), residues: 380 loop : -2.05 (0.41), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.002 0.000 HIS I 43 PHE 0.013 0.001 PHE A 359 TYR 0.019 0.001 TYR F 217 ARG 0.003 0.000 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8100 (p0) cc_final: 0.7895 (p0) REVERT: A 141 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8399 (tt) REVERT: A 167 LEU cc_start: 0.8517 (tt) cc_final: 0.7660 (mp) REVERT: A 183 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 217 TYR cc_start: 0.8331 (t80) cc_final: 0.8058 (t80) REVERT: A 219 ARG cc_start: 0.8636 (ttt180) cc_final: 0.7953 (ttt-90) REVERT: A 367 LEU cc_start: 0.8279 (tp) cc_final: 0.8051 (tp) REVERT: A 369 MET cc_start: 0.8659 (ttm) cc_final: 0.8349 (ttt) REVERT: B 35 PHE cc_start: 0.8828 (t80) cc_final: 0.8496 (t80) REVERT: B 52 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7189 (p0) REVERT: C 94 LYS cc_start: 0.8943 (tptt) cc_final: 0.8477 (tppt) REVERT: D 18 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8579 (tp40) REVERT: D 22 GLU cc_start: 0.8558 (pm20) cc_final: 0.7862 (pm20) REVERT: E 25 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7127 (mp10) REVERT: E 41 PHE cc_start: 0.9310 (m-80) cc_final: 0.9059 (m-80) REVERT: E 50 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: E 56 MET cc_start: 0.8714 (tpt) cc_final: 0.8273 (tpt) REVERT: F 87 ASP cc_start: 0.8080 (p0) cc_final: 0.7849 (p0) REVERT: F 132 ASP cc_start: 0.8818 (p0) cc_final: 0.8433 (p0) REVERT: F 167 LEU cc_start: 0.8538 (tt) cc_final: 0.7706 (mp) REVERT: F 183 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8306 (mm) REVERT: F 219 ARG cc_start: 0.8502 (ttt-90) cc_final: 0.7663 (ttt-90) REVERT: F 241 GLN cc_start: 0.8456 (mm110) cc_final: 0.8188 (mp10) REVERT: F 369 MET cc_start: 0.8682 (ttm) cc_final: 0.8358 (ttt) REVERT: G 35 PHE cc_start: 0.8848 (t80) cc_final: 0.8530 (t80) REVERT: G 52 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7427 (p0) REVERT: I 18 GLN cc_start: 0.9160 (mm-40) cc_final: 0.8777 (tp40) REVERT: J 41 PHE cc_start: 0.9202 (m-80) cc_final: 0.8908 (m-80) REVERT: J 56 MET cc_start: 0.8563 (tpt) cc_final: 0.8077 (tpt) outliers start: 43 outliers final: 32 residues processed: 204 average time/residue: 0.1667 time to fit residues: 46.8047 Evaluate side-chains 201 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 163 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 127 GLU Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 40 MET Chi-restraints excluded: chain J residue 34 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 78 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7422 Z= 0.275 Angle : 0.829 20.567 10053 Z= 0.388 Chirality : 0.046 0.165 1141 Planarity : 0.004 0.055 1272 Dihedral : 6.811 77.956 999 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 5.63 % Allowed : 31.71 % Favored : 62.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.30), residues: 888 helix: -1.13 (0.36), residues: 210 sheet: -1.93 (0.26), residues: 380 loop : -2.06 (0.43), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 100 HIS 0.003 0.000 HIS D 43 PHE 0.017 0.001 PHE A 359 TYR 0.015 0.001 TYR F 217 ARG 0.003 0.000 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8437 (p0) cc_final: 0.8148 (p0) REVERT: A 183 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8346 (mm) REVERT: A 217 TYR cc_start: 0.8406 (t80) cc_final: 0.8174 (t80) REVERT: A 219 ARG cc_start: 0.8642 (ttt180) cc_final: 0.8163 (ttt-90) REVERT: A 367 LEU cc_start: 0.8343 (tp) cc_final: 0.8123 (tp) REVERT: A 369 MET cc_start: 0.8685 (ttm) cc_final: 0.8346 (ttt) REVERT: B 35 PHE cc_start: 0.8853 (t80) cc_final: 0.8506 (t80) REVERT: B 52 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7126 (p0) REVERT: C 94 LYS cc_start: 0.8959 (tptt) cc_final: 0.8506 (tppt) REVERT: D 18 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8581 (tp40) REVERT: D 22 GLU cc_start: 0.8637 (pm20) cc_final: 0.7930 (pm20) REVERT: E 25 GLN cc_start: 0.7656 (tp-100) cc_final: 0.7133 (mp10) REVERT: E 41 PHE cc_start: 0.9322 (m-80) cc_final: 0.9079 (m-80) REVERT: E 50 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: E 56 MET cc_start: 0.8633 (tpt) cc_final: 0.8137 (tpt) REVERT: F 87 ASP cc_start: 0.8365 (p0) cc_final: 0.8042 (p0) REVERT: F 183 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8437 (mm) REVERT: F 369 MET cc_start: 0.8701 (ttm) cc_final: 0.8344 (ttt) REVERT: G 35 PHE cc_start: 0.8839 (t80) cc_final: 0.8535 (t80) REVERT: G 52 ASN cc_start: 0.7645 (OUTLIER) cc_final: 0.7176 (p0) REVERT: I 18 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8786 (tp40) REVERT: J 41 PHE cc_start: 0.9214 (m-80) cc_final: 0.8922 (m-80) REVERT: J 50 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7768 (mp10) outliers start: 44 outliers final: 35 residues processed: 193 average time/residue: 0.1648 time to fit residues: 44.0281 Evaluate side-chains 199 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 158 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 43 HIS Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 50 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7422 Z= 0.216 Angle : 0.807 19.908 10053 Z= 0.374 Chirality : 0.045 0.171 1141 Planarity : 0.004 0.057 1272 Dihedral : 6.574 78.380 999 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.86 % Allowed : 32.99 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.30), residues: 888 helix: -1.07 (0.36), residues: 210 sheet: -1.82 (0.27), residues: 380 loop : -2.01 (0.43), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 260 HIS 0.001 0.000 HIS G 43 PHE 0.015 0.001 PHE A 359 TYR 0.018 0.001 TYR F 217 ARG 0.003 0.000 ARG G 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 87 ASP cc_start: 0.8279 (p0) cc_final: 0.8000 (p0) REVERT: A 167 LEU cc_start: 0.8430 (tt) cc_final: 0.7601 (mp) REVERT: A 183 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 217 TYR cc_start: 0.8377 (t80) cc_final: 0.8146 (t80) REVERT: A 219 ARG cc_start: 0.8670 (ttt180) cc_final: 0.7990 (ttt-90) REVERT: A 367 LEU cc_start: 0.8358 (tp) cc_final: 0.8143 (tp) REVERT: A 369 MET cc_start: 0.8658 (ttm) cc_final: 0.8322 (ttt) REVERT: B 35 PHE cc_start: 0.8833 (t80) cc_final: 0.8500 (t80) REVERT: B 52 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7101 (p0) REVERT: C 94 LYS cc_start: 0.8907 (tptt) cc_final: 0.8484 (tppt) REVERT: D 18 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8559 (tp40) REVERT: D 22 GLU cc_start: 0.8629 (pm20) cc_final: 0.7915 (pm20) REVERT: E 25 GLN cc_start: 0.7630 (tp-100) cc_final: 0.7343 (mp10) REVERT: E 41 PHE cc_start: 0.9324 (m-80) cc_final: 0.9082 (m-80) REVERT: E 56 MET cc_start: 0.8640 (tpt) cc_final: 0.8158 (tpt) REVERT: F 87 ASP cc_start: 0.8233 (p0) cc_final: 0.7966 (p0) REVERT: F 132 ASP cc_start: 0.8851 (p0) cc_final: 0.8411 (p0) REVERT: F 167 LEU cc_start: 0.8520 (tt) cc_final: 0.7730 (mp) REVERT: F 183 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8371 (mm) REVERT: F 241 GLN cc_start: 0.8482 (mm110) cc_final: 0.8206 (mp10) REVERT: F 369 MET cc_start: 0.8660 (ttm) cc_final: 0.8282 (ttt) REVERT: G 35 PHE cc_start: 0.8868 (t80) cc_final: 0.8535 (t80) REVERT: G 52 ASN cc_start: 0.7657 (OUTLIER) cc_final: 0.7147 (p0) REVERT: I 18 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8777 (tp40) REVERT: J 38 ASN cc_start: 0.8456 (m-40) cc_final: 0.8227 (m-40) REVERT: J 41 PHE cc_start: 0.9215 (m-80) cc_final: 0.8920 (m-80) REVERT: J 50 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7637 (mp10) outliers start: 38 outliers final: 30 residues processed: 195 average time/residue: 0.1696 time to fit residues: 45.3556 Evaluate side-chains 199 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 184 ASN Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain D residue 17 HIS Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 49 HIS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 183 LEU Chi-restraints excluded: chain F residue 184 ASN Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain J residue 34 THR Chi-restraints excluded: chain J residue 50 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.179257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135574 restraints weight = 8557.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133704 restraints weight = 10135.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.135438 restraints weight = 9421.741| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7422 Z= 0.188 Angle : 0.787 18.636 10053 Z= 0.363 Chirality : 0.044 0.167 1141 Planarity : 0.004 0.059 1272 Dihedral : 6.226 80.283 999 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer: Outliers : 4.60 % Allowed : 32.99 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.30), residues: 888 helix: -1.01 (0.36), residues: 210 sheet: -1.69 (0.27), residues: 380 loop : -1.99 (0.43), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 260 HIS 0.001 0.000 HIS G 43 PHE 0.015 0.001 PHE A 359 TYR 0.019 0.001 TYR F 217 ARG 0.003 0.000 ARG G 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1730.81 seconds wall clock time: 32 minutes 27.93 seconds (1947.93 seconds total)