Starting phenix.real_space_refine on Fri Mar 15 06:38:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x2c_32964/03_2024/7x2c_32964_updated.pdb" } resolution = 3.2 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= -0.005 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2939 atoms to isotropic. 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 S 56 5.16 5 Cl 2 4.86 5 C 5071 2.51 5 N 1341 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 85": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7953 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2167 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 279, 2156 Classifications: {'peptide': 279} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 2197 Chain: "A" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1824 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 2538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Conformer: "B" Number of residues, atoms: 339, 2526 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 67 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 9, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 bond proxies already assigned to first conformer: 2559 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 401 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 953 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 1, 'G3C': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 6.52, per 1000 atoms: 0.82 Number of scatterers: 7953 At special positions: 0 Unit cell: (77.177, 101.091, 123.918, 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) Cl 2 17.00 S 56 16.00 O 1483 8.00 N 1341 7.00 C 5071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.03 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: 3.13 Conformation dependent library (CDL) restraints added in 2.4 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 40.4% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'F' and resid 21 through 50 removed outlier: 3.522A pdb=" N VAL F 48 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 58 through 87 removed outlier: 3.815A pdb=" N PHE F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 93 through 126 removed outlier: 3.615A pdb=" N CYS F 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN F 97 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ILE F 104 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET F 105 " --> pdb=" O PHE F 102 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR F 108 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU F 112 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASN F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 Processing helix chain 'F' and resid 137 through 153 Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 192 through 240 Proline residue: F 206 - end of helix Processing helix chain 'F' and resid 265 through 297 removed outlier: 3.883A pdb=" N PHE F 281 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 4.177A pdb=" N SER F 324 " --> pdb=" O GLY F 320 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER F 325 " --> pdb=" O TRP F 321 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 343 removed outlier: 3.580A pdb=" N LYS F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.675A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.636A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.439A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.829A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.311A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.821A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.028A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.988A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.526A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.419A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 52 removed outlier: 4.106A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.144A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1080 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: 2.15 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2575 1.34 - 1.46: 2028 1.46 - 1.58: 3444 1.58 - 1.70: 6 1.70 - 1.82: 77 Bond restraints: 8130 Sorted by residual: bond pdb=" C06 G3C F 503 " pdb=" C07 G3C F 503 " ideal model delta sigma weight residual 1.523 1.650 -0.127 2.00e-02 2.50e+03 4.06e+01 bond pdb=" C07 G3C F 502 " pdb=" C08 G3C F 502 " ideal model delta sigma weight residual 1.510 1.637 -0.127 2.00e-02 2.50e+03 4.03e+01 bond pdb=" C07 G3C F 503 " pdb=" C08 G3C F 503 " ideal model delta sigma weight residual 1.510 1.632 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C06 G3C F 502 " pdb=" C07 G3C F 502 " ideal model delta sigma weight residual 1.523 1.639 -0.116 2.00e-02 2.50e+03 3.37e+01 bond pdb=" C13 CLR F 501 " pdb=" C17 CLR F 501 " ideal model delta sigma weight residual 1.550 1.438 0.112 2.00e-02 2.50e+03 3.13e+01 ... (remaining 8125 not shown) Histogram of bond angle deviations from ideal: 95.14 - 102.96: 43 102.96 - 110.78: 2791 110.78 - 118.60: 3630 118.60 - 126.42: 4477 126.42 - 134.24: 139 Bond angle restraints: 11080 Sorted by residual: angle pdb=" C23 CLR F 501 " pdb=" C24 CLR F 501 " pdb=" C25 CLR F 501 " ideal model delta sigma weight residual 115.14 103.15 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C GLY A 353 " pdb=" N ASP A 354 " pdb=" CA ASP A 354 " ideal model delta sigma weight residual 122.61 128.39 -5.78 1.56e+00 4.11e-01 1.37e+01 angle pdb=" N GLY B 319 " pdb=" CA GLY B 319 " pdb=" C GLY B 319 " ideal model delta sigma weight residual 110.87 116.55 -5.68 1.54e+00 4.22e-01 1.36e+01 angle pdb=" C TYR F 204 " pdb=" N ILE F 205 " pdb=" CA ILE F 205 " ideal model delta sigma weight residual 122.13 116.03 6.10 1.85e+00 2.92e-01 1.09e+01 angle pdb=" C17 CLR F 501 " pdb=" C20 CLR F 501 " pdb=" C22 CLR F 501 " ideal model delta sigma weight residual 109.45 99.78 9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 11075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4409 17.95 - 35.90: 350 35.90 - 53.85: 62 53.85 - 71.80: 13 71.80 - 89.75: 3 Dihedral angle restraints: 4837 sinusoidal: 1820 harmonic: 3017 Sorted by residual: dihedral pdb=" CB CYS F 96 " pdb=" SG CYS F 96 " pdb=" SG CYS F 186 " pdb=" CB CYS F 186 " ideal model delta sinusoidal sigma weight residual 93.00 139.20 -46.20 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CA ILE F 201 " pdb=" C ILE F 201 " pdb=" N SER F 202 " pdb=" CA SER F 202 " ideal model delta harmonic sigma weight residual 180.00 -158.95 -21.05 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA MET F 135 " pdb=" C MET F 135 " pdb=" N THR F 136 " pdb=" CA THR F 136 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 4834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 1271 0.135 - 0.270: 2 0.270 - 0.405: 2 0.405 - 0.540: 0 0.540 - 0.675: 2 Chirality restraints: 1277 Sorted by residual: chirality pdb=" C13 CLR F 501 " pdb=" C12 CLR F 501 " pdb=" C14 CLR F 501 " pdb=" C17 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.93 -2.26 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" C10 CLR F 501 " pdb=" C1 CLR F 501 " pdb=" C5 CLR F 501 " pdb=" C9 CLR F 501 " both_signs ideal model delta sigma weight residual False -2.85 -2.23 -0.62 2.00e-01 2.50e+01 9.64e+00 chirality pdb=" C07 G3C F 502 " pdb=" C06 G3C F 502 " pdb=" C08 G3C F 502 " pdb=" C15 G3C F 502 " both_signs ideal model delta sigma weight residual False -2.44 -2.75 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1274 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 205 " 0.052 5.00e-02 4.00e+02 7.88e-02 9.92e+00 pdb=" N PRO F 206 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 206 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 206 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 201 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C ILE F 201 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE F 201 " -0.019 2.00e-02 2.50e+03 pdb=" N SER F 202 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 327 " 0.047 5.00e-02 4.00e+02 7.08e-02 8.02e+00 pdb=" N PRO F 328 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 328 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 328 " 0.040 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 128 2.66 - 3.22: 7596 3.22 - 3.78: 12552 3.78 - 4.34: 16832 4.34 - 4.90: 28156 Nonbonded interactions: 65264 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.102 2.440 nonbonded pdb=" OD1 ASP A 229 " pdb=" OG1 THR E 111 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR B 321 " pdb=" N GLY B 324 " model vdw 2.222 2.520 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.246 2.440 nonbonded pdb=" OG SER F 198 " pdb=" O01 G3C F 503 " model vdw 2.255 2.440 ... (remaining 65259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 1.750 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.550 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 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 : 0.006 0.127 8130 Z= 0.405 Angle : 0.705 11.992 11080 Z= 0.358 Chirality : 0.051 0.675 1277 Planarity : 0.005 0.079 1403 Dihedral : 13.490 89.746 2870 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.48 % Allowed : 0.24 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1020 helix: 1.81 (0.26), residues: 406 sheet: 0.52 (0.33), residues: 224 loop : -0.48 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.001 PHE A 212 TYR 0.021 0.001 TYR B 59 ARG 0.005 0.000 ARG F 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 29 GLN cc_start: 0.7752 (tp-100) cc_final: 0.7120 (tm-30) REVERT: A 386 MET cc_start: 0.7988 (ttm) cc_final: 0.7455 (tpp) REVERT: B 137 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7337 (mmm160) REVERT: B 148 CYS cc_start: 0.8391 (t) cc_final: 0.8171 (t) REVERT: B 217 MET cc_start: 0.6838 (tmm) cc_final: 0.6290 (tmm) REVERT: D 41 CYS cc_start: 0.7902 (m) cc_final: 0.7668 (m) REVERT: D 47 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6891 (mp0) REVERT: E 82 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1868 time to fit residues: 40.4350 Evaluate side-chains 139 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 GLN B 237 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8130 Z= 0.281 Angle : 0.571 6.788 11080 Z= 0.308 Chirality : 0.043 0.153 1277 Planarity : 0.005 0.073 1403 Dihedral : 4.489 28.164 1203 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.69 % Allowed : 8.59 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1020 helix: 1.74 (0.25), residues: 416 sheet: 0.52 (0.33), residues: 209 loop : -0.44 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 63 HIS 0.007 0.002 HIS F 53 PHE 0.015 0.002 PHE F 289 TYR 0.027 0.002 TYR B 59 ARG 0.003 0.000 ARG D 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 148 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 ARG cc_start: 0.8059 (ttt-90) cc_final: 0.7537 (tpt-90) REVERT: A 294 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7655 (mm110) REVERT: B 49 ARG cc_start: 0.6394 (mmt180) cc_final: 0.6194 (mmt180) REVERT: B 148 CYS cc_start: 0.8532 (t) cc_final: 0.8316 (t) REVERT: B 217 MET cc_start: 0.6469 (tmm) cc_final: 0.6018 (tmm) REVERT: B 259 GLN cc_start: 0.6852 (mt0) cc_final: 0.6622 (mm-40) REVERT: B 274 THR cc_start: 0.8080 (m) cc_final: 0.7713 (p) REVERT: D 41 CYS cc_start: 0.8014 (m) cc_final: 0.7813 (m) REVERT: D 47 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6757 (mp0) REVERT: E 82 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7672 (tm-30) outliers start: 10 outliers final: 9 residues processed: 151 average time/residue: 0.1919 time to fit residues: 39.8110 Evaluate side-chains 145 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 181 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 50.0000 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8130 Z= 0.197 Angle : 0.523 5.830 11080 Z= 0.279 Chirality : 0.041 0.198 1277 Planarity : 0.004 0.065 1403 Dihedral : 4.340 31.229 1203 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.18 % Allowed : 11.49 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1020 helix: 1.88 (0.26), residues: 411 sheet: 0.51 (0.34), residues: 204 loop : -0.48 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 63 HIS 0.006 0.001 HIS F 53 PHE 0.019 0.001 PHE F 288 TYR 0.013 0.001 TYR B 59 ARG 0.002 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7667 (mm110) REVERT: A 386 MET cc_start: 0.8040 (ttm) cc_final: 0.7524 (tpp) REVERT: B 217 MET cc_start: 0.6032 (tmm) cc_final: 0.5658 (tmm) REVERT: D 41 CYS cc_start: 0.8054 (m) cc_final: 0.7838 (m) REVERT: D 47 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6809 (mp0) REVERT: E 82 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7664 (tm-30) outliers start: 14 outliers final: 9 residues processed: 151 average time/residue: 0.2006 time to fit residues: 41.0561 Evaluate side-chains 143 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0000 chunk 67 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN E 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8130 Z= 0.195 Angle : 0.523 8.882 11080 Z= 0.278 Chirality : 0.041 0.167 1277 Planarity : 0.004 0.061 1403 Dihedral : 4.297 34.547 1203 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.54 % Allowed : 13.06 % Favored : 84.40 % 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: 1.03 (0.26), residues: 1020 helix: 1.93 (0.26), residues: 410 sheet: 0.48 (0.34), residues: 204 loop : -0.46 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 63 HIS 0.006 0.001 HIS F 53 PHE 0.014 0.001 PHE F 288 TYR 0.008 0.001 TYR F 194 ARG 0.009 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7271 (mtm-85) REVERT: A 294 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7794 (mm-40) REVERT: A 386 MET cc_start: 0.8061 (ttm) cc_final: 0.7543 (tpp) REVERT: B 171 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 217 MET cc_start: 0.6008 (tmm) cc_final: 0.5644 (tmm) REVERT: B 220 GLN cc_start: 0.7989 (tt0) cc_final: 0.7763 (tt0) REVERT: D 41 CYS cc_start: 0.8150 (m) cc_final: 0.7912 (m) REVERT: D 47 GLU cc_start: 0.7468 (mt-10) cc_final: 0.6876 (mp0) REVERT: E 82 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7644 (tm-30) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.1875 time to fit residues: 39.1935 Evaluate side-chains 151 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 31 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 23 ASN B 119 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8130 Z= 0.247 Angle : 0.542 8.893 11080 Z= 0.289 Chirality : 0.042 0.167 1277 Planarity : 0.004 0.061 1403 Dihedral : 4.348 34.880 1203 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.66 % Allowed : 14.51 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1020 helix: 1.87 (0.26), residues: 416 sheet: 0.46 (0.35), residues: 204 loop : -0.41 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 63 HIS 0.006 0.001 HIS F 53 PHE 0.014 0.002 PHE F 289 TYR 0.009 0.001 TYR F 194 ARG 0.006 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7505 (ttm170) cc_final: 0.7239 (mtm-85) REVERT: A 294 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7696 (mm110) REVERT: A 386 MET cc_start: 0.8035 (ttm) cc_final: 0.7511 (tpp) REVERT: B 68 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7657 (mtp180) REVERT: B 217 MET cc_start: 0.6171 (tmm) cc_final: 0.5793 (tmm) REVERT: D 41 CYS cc_start: 0.8164 (m) cc_final: 0.7937 (m) REVERT: D 47 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6888 (mp0) REVERT: E 82 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7668 (tm-30) outliers start: 18 outliers final: 15 residues processed: 147 average time/residue: 0.1968 time to fit residues: 40.3003 Evaluate side-chains 149 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.0060 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 30.0000 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN E 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8130 Z= 0.172 Angle : 0.507 7.244 11080 Z= 0.270 Chirality : 0.041 0.167 1277 Planarity : 0.004 0.058 1403 Dihedral : 4.232 37.565 1203 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.14 % Allowed : 15.11 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1020 helix: 1.96 (0.26), residues: 413 sheet: 0.39 (0.35), residues: 206 loop : -0.41 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 63 HIS 0.005 0.001 HIS F 53 PHE 0.014 0.001 PHE F 288 TYR 0.006 0.001 TYR E 60 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7522 (ttm170) cc_final: 0.7287 (mtm-85) REVERT: A 294 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7713 (mm110) REVERT: A 386 MET cc_start: 0.8028 (ttm) cc_final: 0.7501 (tpp) REVERT: B 217 MET cc_start: 0.6162 (tmm) cc_final: 0.5794 (tmm) REVERT: B 303 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7441 (m-30) REVERT: D 41 CYS cc_start: 0.8149 (m) cc_final: 0.7916 (m) REVERT: D 47 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6960 (mp0) REVERT: E 82 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7654 (tm-30) outliers start: 22 outliers final: 16 residues processed: 151 average time/residue: 0.1841 time to fit residues: 38.5388 Evaluate side-chains 157 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 31 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 230 ASN E 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8130 Z= 0.300 Angle : 0.573 7.721 11080 Z= 0.307 Chirality : 0.043 0.157 1277 Planarity : 0.004 0.060 1403 Dihedral : 4.410 35.633 1203 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.26 % Allowed : 15.11 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.27), residues: 1020 helix: 1.78 (0.26), residues: 416 sheet: 0.25 (0.35), residues: 214 loop : -0.28 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.014 0.002 PHE F 289 TYR 0.010 0.001 TYR A 360 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7521 (ttm170) cc_final: 0.7244 (mtm-85) REVERT: A 386 MET cc_start: 0.8064 (ttm) cc_final: 0.7547 (tpp) REVERT: B 217 MET cc_start: 0.6450 (tmm) cc_final: 0.6036 (tmm) REVERT: D 41 CYS cc_start: 0.8273 (m) cc_final: 0.7995 (m) REVERT: D 47 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6864 (mp0) REVERT: E 82 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7624 (tm-30) outliers start: 23 outliers final: 20 residues processed: 143 average time/residue: 0.1936 time to fit residues: 38.2982 Evaluate side-chains 151 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 131 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN B 259 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8130 Z= 0.152 Angle : 0.507 6.973 11080 Z= 0.268 Chirality : 0.040 0.157 1277 Planarity : 0.004 0.058 1403 Dihedral : 4.202 39.395 1203 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.66 % Allowed : 16.57 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.27), residues: 1020 helix: 2.00 (0.26), residues: 411 sheet: 0.11 (0.33), residues: 221 loop : -0.35 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS F 53 PHE 0.012 0.001 PHE F 289 TYR 0.009 0.001 TYR B 124 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8006 (ttm) cc_final: 0.7471 (tpp) REVERT: B 68 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7817 (mtp180) REVERT: B 217 MET cc_start: 0.6371 (tmm) cc_final: 0.5978 (tmm) REVERT: D 41 CYS cc_start: 0.8167 (m) cc_final: 0.7906 (m) REVERT: D 47 GLU cc_start: 0.7410 (mt-10) cc_final: 0.6907 (mp0) REVERT: E 82 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7651 (tm-30) outliers start: 18 outliers final: 17 residues processed: 149 average time/residue: 0.1915 time to fit residues: 39.0896 Evaluate side-chains 156 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0670 chunk 91 optimal weight: 0.0970 chunk 53 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 chunk 69 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8130 Z= 0.146 Angle : 0.509 7.836 11080 Z= 0.268 Chirality : 0.040 0.153 1277 Planarity : 0.004 0.056 1403 Dihedral : 4.105 41.879 1203 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.30 % Allowed : 17.90 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 1020 helix: 1.86 (0.26), residues: 419 sheet: 0.02 (0.34), residues: 219 loop : -0.31 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS F 53 PHE 0.011 0.001 PHE F 288 TYR 0.008 0.001 TYR B 124 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7328 (ttm110) cc_final: 0.6906 (mtm-85) REVERT: A 386 MET cc_start: 0.8026 (ttm) cc_final: 0.7495 (tpp) REVERT: B 68 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7787 (mtp180) REVERT: B 101 MET cc_start: 0.8835 (mtt) cc_final: 0.8549 (mtp) REVERT: B 217 MET cc_start: 0.6393 (tmm) cc_final: 0.5998 (tmm) REVERT: D 41 CYS cc_start: 0.8126 (m) cc_final: 0.7871 (m) REVERT: D 47 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6879 (mp0) REVERT: E 82 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7829 (tm-30) outliers start: 15 outliers final: 13 residues processed: 139 average time/residue: 0.1992 time to fit residues: 38.0932 Evaluate side-chains 145 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 132 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 102 PHE Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 307 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN E 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8130 Z= 0.257 Angle : 0.560 7.012 11080 Z= 0.297 Chirality : 0.042 0.141 1277 Planarity : 0.004 0.057 1403 Dihedral : 4.311 39.031 1203 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.42 % Allowed : 18.02 % Favored : 79.56 % 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: 0.94 (0.27), residues: 1020 helix: 1.76 (0.26), residues: 422 sheet: 0.13 (0.34), residues: 214 loop : -0.28 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.005 0.001 HIS B 183 PHE 0.017 0.002 PHE F 288 TYR 0.010 0.001 TYR F 194 ARG 0.004 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 133 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 226 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6905 (mtm-85) REVERT: A 386 MET cc_start: 0.8055 (ttm) cc_final: 0.7534 (tpp) REVERT: B 68 ARG cc_start: 0.8275 (mtp180) cc_final: 0.7453 (mtp-110) REVERT: B 101 MET cc_start: 0.8907 (mtt) cc_final: 0.8572 (mtp) REVERT: B 217 MET cc_start: 0.6425 (tmm) cc_final: 0.6048 (tmm) REVERT: D 41 CYS cc_start: 0.8263 (m) cc_final: 0.7969 (m) REVERT: D 47 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6916 (mp0) REVERT: E 82 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7654 (tm-30) outliers start: 16 outliers final: 15 residues processed: 140 average time/residue: 0.1866 time to fit residues: 36.0613 Evaluate side-chains 147 residues out of total 883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 308 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 31 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN E 31 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.169174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118280 restraints weight = 26987.179| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 5.26 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8130 Z= 0.170 Angle : 0.525 7.772 11080 Z= 0.276 Chirality : 0.041 0.145 1277 Planarity : 0.004 0.056 1403 Dihedral : 4.246 40.756 1203 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.42 % Allowed : 17.90 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 1020 helix: 1.88 (0.26), residues: 417 sheet: 0.06 (0.34), residues: 219 loop : -0.35 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS F 53 PHE 0.015 0.001 PHE F 288 TYR 0.009 0.001 TYR B 124 ARG 0.005 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.59 seconds wall clock time: 35 minutes 15.17 seconds (2115.17 seconds total)