Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 12:28:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/04_2023/6jnf_9851_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/04_2023/6jnf_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_9851/04_2023/6jnf_9851.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/04_2023/6jnf_9851.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/04_2023/6jnf_9851_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jnf_9851/04_2023/6jnf_9851_updated.pdb" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 4.42, per 1000 atoms: 0.61 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: 2.71 Conformation dependent library (CDL) restraints added in 1.0 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: 0.67 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: 1.72 Time building geometry restraints manager: 2.93 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 - 17.26: 3705 17.26 - 34.52: 516 34.52 - 51.78: 100 51.78 - 69.04: 21 69.04 - 86.30: 19 Dihedral angle restraints: 4361 sinusoidal: 1707 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 4358 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.100 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 21.510 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.650 ------------------------------------------------------------------------------- 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 : 17.143 86.302 2641 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 % 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 *********************** 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 : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 202 average time/residue: 0.2006 time to fit residues: 52.8316 Evaluate side-chains 160 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0615 time to fit residues: 1.5147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7882 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7422 Z= 0.175 Angle : 0.768 12.321 10053 Z= 0.373 Chirality : 0.044 0.155 1141 Planarity : 0.005 0.054 1272 Dihedral : 7.082 65.691 987 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.14 % Favored : 89.86 % Rotamer Outliers : 1.53 % 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: -4.98 (0.25), residues: 888 helix: -3.40 (0.24), residues: 206 sheet: -2.95 (0.25), residues: 366 loop : -3.27 (0.32), residues: 316 *********************** 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 184 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 178 average time/residue: 0.1993 time to fit residues: 46.6762 Evaluate side-chains 172 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 162 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0719 time to fit residues: 2.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.7964 moved from start: 0.2514 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= 0.324 Angle : 0.824 12.424 10053 Z= 0.398 Chirality : 0.047 0.168 1141 Planarity : 0.005 0.048 1272 Dihedral : 7.321 71.231 987 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer Outliers : 3.71 % 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: -4.33 (0.27), residues: 888 helix: -2.40 (0.31), residues: 208 sheet: -2.82 (0.26), residues: 368 loop : -2.86 (0.36), residues: 312 *********************** 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 195 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 185 average time/residue: 0.1800 time to fit residues: 45.1431 Evaluate side-chains 168 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 155 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0664 time to fit residues: 2.8086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.0010 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- 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 311 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN I 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.175 Angle : 0.774 12.781 10053 Z= 0.361 Chirality : 0.045 0.206 1141 Planarity : 0.004 0.052 1272 Dihedral : 6.425 56.358 987 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer Outliers : 2.05 % 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: -3.86 (0.27), residues: 888 helix: -1.93 (0.33), residues: 210 sheet: -2.43 (0.26), residues: 366 loop : -2.82 (0.36), residues: 312 *********************** 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 182 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 176 average time/residue: 0.1767 time to fit residues: 42.1442 Evaluate side-chains 167 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0659 time to fit residues: 2.0310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 43 optimal weight: 0.3980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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** E 25 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: 0.7941 moved from start: 0.3062 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= 0.290 Angle : 0.793 12.337 10053 Z= 0.381 Chirality : 0.046 0.168 1141 Planarity : 0.004 0.055 1272 Dihedral : 6.615 50.923 987 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer Outliers : 3.58 % 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: -3.58 (0.28), residues: 888 helix: -1.48 (0.36), residues: 210 sheet: -2.39 (0.26), residues: 366 loop : -2.66 (0.37), residues: 312 *********************** 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 189 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 182 average time/residue: 0.2088 time to fit residues: 52.8961 Evaluate side-chains 170 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0763 time to fit residues: 3.3030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- 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 17 HIS ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7422 Z= 0.188 Angle : 0.780 14.091 10053 Z= 0.361 Chirality : 0.045 0.162 1141 Planarity : 0.004 0.056 1272 Dihedral : 5.988 42.812 987 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer Outliers : 1.41 % 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: -3.26 (0.29), residues: 888 helix: -1.32 (0.36), residues: 210 sheet: -2.11 (0.27), residues: 366 loop : -2.53 (0.37), residues: 312 *********************** 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 175 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 170 average time/residue: 0.1837 time to fit residues: 42.4515 Evaluate side-chains 164 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0697 time to fit residues: 2.2176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 0.0370 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.3401 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= 0.182 Angle : 0.793 13.629 10053 Z= 0.367 Chirality : 0.045 0.156 1141 Planarity : 0.004 0.053 1272 Dihedral : 5.602 39.760 987 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.29), residues: 888 helix: -1.04 (0.37), residues: 198 sheet: -1.87 (0.27), residues: 380 loop : -2.19 (0.39), residues: 310 *********************** 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 180 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 175 average time/residue: 0.1946 time to fit residues: 45.6386 Evaluate side-chains 161 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 154 time to evaluate : 0.868 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0698 time to fit residues: 2.0477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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** A 241 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7422 Z= 0.341 Angle : 0.852 13.029 10053 Z= 0.408 Chirality : 0.048 0.172 1141 Planarity : 0.004 0.054 1272 Dihedral : 6.310 40.612 987 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer Outliers : 2.05 % 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: -3.00 (0.29), residues: 888 helix: -1.06 (0.37), residues: 208 sheet: -2.07 (0.26), residues: 382 loop : -2.18 (0.40), residues: 298 *********************** 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 178 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 170 average time/residue: 0.1889 time to fit residues: 43.3574 Evaluate side-chains 165 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0709 time to fit residues: 2.2416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7894 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7422 Z= 0.219 Angle : 0.866 19.313 10053 Z= 0.394 Chirality : 0.046 0.185 1141 Planarity : 0.004 0.055 1272 Dihedral : 5.886 42.433 987 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.49 % Favored : 88.51 % Rotamer Outliers : 0.26 % 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: -2.93 (0.30), residues: 888 helix: -1.17 (0.36), residues: 210 sheet: -1.91 (0.27), residues: 380 loop : -2.20 (0.40), residues: 298 *********************** 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 168 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 166 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 168 average time/residue: 0.1885 time to fit residues: 42.6194 Evaluate side-chains 159 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0674 time to fit residues: 1.3075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7935 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7422 Z= 0.299 Angle : 0.895 20.728 10053 Z= 0.414 Chirality : 0.048 0.238 1141 Planarity : 0.004 0.054 1272 Dihedral : 6.224 43.823 987 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.19 % Favored : 85.81 % Rotamer Outliers : 0.13 % 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: -3.04 (0.30), residues: 888 helix: -1.28 (0.36), residues: 222 sheet: -2.05 (0.26), residues: 380 loop : -2.15 (0.42), residues: 286 ********************** 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 159 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 159 average time/residue: 0.1762 time to fit residues: 38.5349 Evaluate side-chains 157 residues out of total 782 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0673 time to fit residues: 1.2933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 69 optimal weight: 0.0000 chunk 29 optimal weight: 0.0470 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4204 r_free = 0.4204 target = 0.178927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135946 restraints weight = 8497.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.134635 restraints weight = 10396.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.136053 restraints weight = 9254.710| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7422 Z= 0.190 Angle : 0.854 20.071 10053 Z= 0.390 Chirality : 0.045 0.200 1141 Planarity : 0.004 0.054 1272 Dihedral : 5.602 42.140 987 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer Outliers : 0.64 % 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: -2.83 (0.30), residues: 888 helix: -1.19 (0.35), residues: 226 sheet: -1.82 (0.26), residues: 380 loop : -2.12 (0.43), residues: 282 =============================================================================== Job complete usr+sys time: 1637.47 seconds wall clock time: 30 minutes 27.93 seconds (1827.93 seconds total)