Starting phenix.real_space_refine on Thu Mar 14 21:32:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/03_2024/6jmr_9850_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 6190 2.51 5 N 1643 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 76": "OD1" <-> "OD2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 189": "OD1" <-> "OD2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ASP 229": "OD1" <-> "OD2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B GLU 413": "OE1" <-> "OE2" Residue "B ASP 470": "OD1" <-> "OD2" Residue "B ASP 475": "OD1" <-> "OD2" Residue "B GLU 514": "OE1" <-> "OE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B PHE 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 111": "OE1" <-> "OE2" Residue "D PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9809 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1646 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 199} Chain breaks: 1 Chain: "F" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 11, 'TRANS': 206} Chain: "B" Number of atoms: 3276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3276 Classifications: {'peptide': 421} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain: "C" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1526 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 16, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'UNK:plan-1': 31} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1597 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 9, 'TRANS': 209} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.82, per 1000 atoms: 0.59 Number of scatterers: 9809 At special positions: 0 Unit cell: (84.93, 137.08, 140.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 32 16.00 O 1944 8.00 N 1643 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 146 " - pdb=" SG CYS E 201 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 200 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 200 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 381 " " NAG B 703 " - " ASN B 424 " " NAG B 704 " - " ASN B 506 " " NAG B 705 " - " ASN B 365 " Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2398 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 24 sheets defined 11.9% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'F' and resid 127 through 132 removed outlier: 3.658A pdb=" N THR F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 127 through 132' Processing helix chain 'F' and resid 188 through 192 Processing helix chain 'B' and resid 230 through 233 No H-bonds generated for 'chain 'B' and resid 230 through 233' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 247 through 254 removed outlier: 3.524A pdb=" N SER B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.800A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 339 removed outlier: 3.544A pdb=" N ASP B 332 " --> pdb=" O THR B 328 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TRP B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.548A pdb=" N ALA B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLU B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR B 367 " --> pdb=" O TRP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 415 through 425 removed outlier: 3.814A pdb=" N THR B 420 " --> pdb=" O LYS B 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.598A pdb=" N THR B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 495 No H-bonds generated for 'chain 'B' and resid 493 through 495' Processing helix chain 'B' and resid 509 through 512 No H-bonds generated for 'chain 'B' and resid 509 through 512' Processing helix chain 'B' and resid 520 through 532 removed outlier: 3.549A pdb=" N ARG B 525 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 528 " --> pdb=" O ARG B 524 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLN B 529 " --> pdb=" O ARG B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 538 removed outlier: 3.622A pdb=" N HIS B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 534 through 538' Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 190 through 193 No H-bonds generated for 'chain 'C' and resid 190 through 193' Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 189 through 193 Processing sheet with id= A, first strand: chain 'E' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'E' and resid 46 through 48 removed outlier: 4.172A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 126 through 130 removed outlier: 3.590A pdb=" N LEU E 130 " --> pdb=" O GLY E 145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 145 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 183 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E 150 " --> pdb=" O TYR E 181 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR E 181 " --> pdb=" O GLY E 150 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.155A pdb=" N VAL E 199 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL E 212 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 205 " --> pdb=" O THR E 210 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 175 through 177 removed outlier: 3.643A pdb=" N VAL E 175 " --> pdb=" O THR E 182 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 4 through 6 removed outlier: 3.701A pdb=" N VAL F 19 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE F 77 " --> pdb=" O CYS F 23 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 10 through 12 removed outlier: 9.521A pdb=" N LEU F 11 " --> pdb=" O GLY F 106 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS F 108 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN F 95 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE F 54 " --> pdb=" O TRP F 41 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLN F 43 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 119 through 123 removed outlier: 5.949A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 150 through 155 Processing sheet with id= J, first strand: chain 'B' and resid 259 through 261 Processing sheet with id= K, first strand: chain 'B' and resid 431 through 433 Processing sheet with id= L, first strand: chain 'B' and resid 540 through 542 removed outlier: 3.501A pdb=" N VAL B 566 " --> pdb=" O LEU B 622 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 265 through 267 removed outlier: 6.846A pdb=" N GLN B 279 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.506A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.714A pdb=" N ALA C 91 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 94 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N UNK C 33 " --> pdb=" O UNK C 98 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 125 through 129 removed outlier: 3.881A pdb=" N GLY C 144 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR C 180 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 140 through 143 Processing sheet with id= R, first strand: chain 'C' and resid 199 through 204 Processing sheet with id= S, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.919A pdb=" N ASP D 76 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.606A pdb=" N LYS D 109 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N VAL D 13 " --> pdb=" O LYS D 109 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU D 111 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 91 through 96 removed outlier: 3.715A pdb=" N ILE D 54 " --> pdb=" O TRP D 41 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN D 43 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.705A pdb=" N SER D 122 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 139 " --> pdb=" O PHE D 124 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 159 through 161 removed outlier: 3.836A pdb=" N TRP D 154 " --> pdb=" O ARG D 161 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS D 200 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 213 " --> pdb=" O CYS D 200 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 142 through 145 removed outlier: 6.238A pdb=" N TYR D 179 " --> pdb=" O ASN D 144 " (cutoff:3.500A) 224 hydrogen bonds defined for protein. 582 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: 2.99 Time building geometry restraints manager: 4.15 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: 3130 1.34 - 1.46: 2269 1.46 - 1.58: 4587 1.58 - 1.70: 1 1.70 - 1.81: 46 Bond restraints: 10033 Sorted by residual: bond pdb=" C TYR D 146 " pdb=" N PRO D 147 " ideal model delta sigma weight residual 1.332 1.381 -0.049 1.12e-02 7.97e+03 1.90e+01 bond pdb=" C THR B 459 " pdb=" N LEU B 460 " ideal model delta sigma weight residual 1.329 1.250 0.079 1.86e-02 2.89e+03 1.79e+01 bond pdb=" C GLU E 154 " pdb=" N PRO E 155 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.47e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 7.99e+00 bond pdb=" C GLU C 153 " pdb=" N PRO C 154 " ideal model delta sigma weight residual 1.334 1.365 -0.031 1.11e-02 8.12e+03 7.62e+00 ... (remaining 10028 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.37: 328 106.37 - 113.63: 5676 113.63 - 120.90: 4283 120.90 - 128.16: 3287 128.16 - 135.43: 93 Bond angle restraints: 13667 Sorted by residual: angle pdb=" C VAL E 99 " pdb=" N TYR E 100 " pdb=" CA TYR E 100 " ideal model delta sigma weight residual 120.82 130.62 -9.80 1.50e+00 4.44e-01 4.27e+01 angle pdb=" N PRO E 155 " pdb=" CA PRO E 155 " pdb=" C PRO E 155 " ideal model delta sigma weight residual 112.47 123.04 -10.57 2.06e+00 2.36e-01 2.63e+01 angle pdb=" C LYS B 354 " pdb=" N ASP B 355 " pdb=" CA ASP B 355 " ideal model delta sigma weight residual 122.82 129.76 -6.94 1.42e+00 4.96e-01 2.39e+01 angle pdb=" N VAL E 99 " pdb=" CA VAL E 99 " pdb=" C VAL E 99 " ideal model delta sigma weight residual 109.55 103.30 6.25 1.38e+00 5.25e-01 2.05e+01 angle pdb=" C SER D 7 " pdb=" N PRO D 8 " pdb=" CA PRO D 8 " ideal model delta sigma weight residual 119.84 114.83 5.01 1.25e+00 6.40e-01 1.61e+01 ... (remaining 13662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.59: 5278 15.59 - 31.18: 645 31.18 - 46.77: 118 46.77 - 62.36: 22 62.36 - 77.95: 9 Dihedral angle restraints: 6072 sinusoidal: 2353 harmonic: 3719 Sorted by residual: dihedral pdb=" CA PHE C 151 " pdb=" C PHE C 151 " pdb=" N PRO C 152 " pdb=" CA PRO C 152 " ideal model delta harmonic sigma weight residual 180.00 128.39 51.61 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA TRP B 557 " pdb=" C TRP B 557 " pdb=" N ASP B 558 " pdb=" CA ASP B 558 " ideal model delta harmonic sigma weight residual 180.00 -138.75 -41.25 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA THR F 102 " pdb=" C THR F 102 " pdb=" N PHE F 103 " pdb=" CA PHE F 103 " ideal model delta harmonic sigma weight residual 180.00 143.79 36.21 0 5.00e+00 4.00e-02 5.24e+01 ... (remaining 6069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1205 0.061 - 0.122: 309 0.122 - 0.183: 51 0.183 - 0.245: 2 0.245 - 0.306: 5 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.46 0.06 2.00e-02 2.50e+03 9.44e+00 chirality pdb=" C1 NAG B 705 " pdb=" ND2 ASN B 365 " pdb=" C2 NAG B 705 " pdb=" O5 NAG B 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG B 703 " pdb=" ND2 ASN B 424 " pdb=" C2 NAG B 703 " pdb=" O5 NAG B 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1569 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 151 " 0.085 5.00e-02 4.00e+02 1.29e-01 2.66e+01 pdb=" N PRO C 152 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO C 152 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO C 152 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 8 " -0.061 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO C 9 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 9 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 9 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 154 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO E 155 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 155 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 155 " -0.042 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1977 2.77 - 3.30: 8698 3.30 - 3.84: 16335 3.84 - 4.37: 17624 4.37 - 4.90: 30920 Nonbonded interactions: 75554 Sorted by model distance: nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.239 2.440 nonbonded pdb=" O PHE F 55 " pdb=" OG1 THR F 59 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR B 468 " pdb=" O PRO B 487 " model vdw 2.265 2.440 nonbonded pdb=" O ASP B 271 " pdb=" OG1 THR B 275 " model vdw 2.295 2.440 nonbonded pdb=" O GLY B 462 " pdb=" NH2 ARG B 530 " model vdw 2.296 2.520 ... (remaining 75549 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=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: 0.310 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: 1.980 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.640 Find NCS groups from input model: 0.330 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.007 0.079 10033 Z= 0.425 Angle : 1.057 11.251 13667 Z= 0.593 Chirality : 0.056 0.306 1572 Planarity : 0.008 0.129 1746 Dihedral : 14.087 77.952 3650 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.10 % Favored : 92.82 % Rotamer: Outliers : 0.56 % Allowed : 9.55 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.35 % 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: -4.07 (0.20), residues: 1197 helix: -3.64 (0.26), residues: 142 sheet: -2.19 (0.21), residues: 430 loop : -2.84 (0.20), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 47 HIS 0.010 0.003 HIS B 538 PHE 0.020 0.003 PHE B 551 TYR 0.023 0.003 TYR F 42 ARG 0.010 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 241 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 81 LYS cc_start: 0.7338 (mppt) cc_final: 0.7060 (mptt) REVERT: E 89 ASP cc_start: 0.7289 (m-30) cc_final: 0.6870 (m-30) REVERT: E 177 GLN cc_start: 0.8448 (tt0) cc_final: 0.7914 (pm20) REVERT: F 41 TRP cc_start: 0.8218 (m100) cc_final: 0.7938 (m100) REVERT: F 45 LYS cc_start: 0.8866 (mttt) cc_final: 0.8395 (mmtm) REVERT: F 100 TYR cc_start: 0.7287 (t80) cc_final: 0.6722 (t80) REVERT: F 150 ASN cc_start: 0.8746 (t0) cc_final: 0.8355 (t0) REVERT: B 283 ASN cc_start: 0.8329 (m-40) cc_final: 0.7968 (t0) REVERT: B 300 LYS cc_start: 0.8981 (mttm) cc_final: 0.8636 (mmmt) REVERT: B 387 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8348 (tp40) REVERT: B 413 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6841 (mm-30) REVERT: B 422 TYR cc_start: 0.8092 (t80) cc_final: 0.7451 (t80) REVERT: B 579 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7517 (tm-30) REVERT: C 2 VAL cc_start: 0.6445 (OUTLIER) cc_final: 0.6041 (m) REVERT: C 72 ASP cc_start: 0.8682 (t0) cc_final: 0.8016 (t0) REVERT: C 175 LEU cc_start: 0.8673 (tp) cc_final: 0.8442 (tp) REVERT: C 201 ASN cc_start: 0.6727 (m-40) cc_final: 0.6110 (m110) REVERT: C 212 ASP cc_start: 0.8637 (m-30) cc_final: 0.8296 (m-30) REVERT: C 213 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7636 (tttm) REVERT: D 48 GLN cc_start: 0.8657 (mp-120) cc_final: 0.8420 (mp10) REVERT: D 79 LEU cc_start: 0.8940 (tp) cc_final: 0.8739 (tp) outliers start: 6 outliers final: 3 residues processed: 247 average time/residue: 0.2538 time to fit residues: 83.2575 Evaluate side-chains 148 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 144 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 44 GLN F 95 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 ASN B 322 GLN B 395 ASN B 529 GLN ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 ASN D 43 GLN D 48 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10033 Z= 0.216 Angle : 0.706 9.862 13667 Z= 0.359 Chirality : 0.046 0.239 1572 Planarity : 0.006 0.104 1746 Dihedral : 7.400 52.985 1469 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % 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: -3.19 (0.22), residues: 1197 helix: -2.30 (0.37), residues: 137 sheet: -1.77 (0.23), residues: 444 loop : -2.30 (0.22), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.005 0.001 HIS B 538 PHE 0.021 0.002 PHE F 103 TYR 0.022 0.002 TYR E 94 ARG 0.006 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 86 GLN cc_start: 0.7956 (mp10) cc_final: 0.7486 (mp10) REVERT: E 89 ASP cc_start: 0.7680 (m-30) cc_final: 0.5954 (p0) REVERT: E 154 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 170 HIS cc_start: 0.8987 (m90) cc_final: 0.8762 (m170) REVERT: E 177 GLN cc_start: 0.8223 (tt0) cc_final: 0.7979 (pm20) REVERT: F 45 LYS cc_start: 0.8938 (mttt) cc_final: 0.8533 (mmtm) REVERT: F 66 ASP cc_start: 0.8449 (m-30) cc_final: 0.8244 (m-30) REVERT: F 150 ASN cc_start: 0.8615 (t0) cc_final: 0.8366 (t0) REVERT: F 161 GLN cc_start: 0.8564 (mt0) cc_final: 0.8014 (pm20) REVERT: F 175 ASP cc_start: 0.8795 (p0) cc_final: 0.7831 (p0) REVERT: B 283 ASN cc_start: 0.8408 (m-40) cc_final: 0.8083 (t0) REVERT: B 300 LYS cc_start: 0.8908 (mttm) cc_final: 0.8545 (mmmt) REVERT: B 413 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6905 (mm-30) REVERT: B 422 TYR cc_start: 0.8069 (t80) cc_final: 0.7421 (t80) REVERT: B 456 MET cc_start: 0.8879 (ttp) cc_final: 0.8545 (tmm) REVERT: B 472 ILE cc_start: 0.9381 (mt) cc_final: 0.9142 (mp) REVERT: B 561 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7659 (mm-30) REVERT: C 72 ASP cc_start: 0.8019 (t0) cc_final: 0.7771 (t0) REVERT: C 75 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8379 (mmmm) REVERT: C 77 GLN cc_start: 0.8239 (pm20) cc_final: 0.7749 (pm20) REVERT: C 89 ASP cc_start: 0.8807 (m-30) cc_final: 0.8504 (m-30) REVERT: C 201 ASN cc_start: 0.6413 (m110) cc_final: 0.5541 (m110) REVERT: D 48 GLN cc_start: 0.8492 (mp10) cc_final: 0.8175 (mp10) REVERT: D 89 LEU cc_start: 0.7010 (pt) cc_final: 0.6330 (tt) REVERT: D 190 ASP cc_start: 0.7931 (t0) cc_final: 0.7717 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2238 time to fit residues: 68.2835 Evaluate side-chains 154 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 ASN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 10033 Z= 0.410 Angle : 0.796 9.714 13667 Z= 0.401 Chirality : 0.049 0.220 1572 Planarity : 0.006 0.105 1746 Dihedral : 7.496 48.880 1469 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.09 % Allowed : 5.62 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.26 % 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: -3.08 (0.22), residues: 1197 helix: -2.14 (0.36), residues: 136 sheet: -1.67 (0.24), residues: 416 loop : -2.27 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 194 HIS 0.007 0.002 HIS B 619 PHE 0.024 0.002 PHE B 544 TYR 0.032 0.003 TYR E 94 ARG 0.015 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 89 ASP cc_start: 0.7965 (m-30) cc_final: 0.6178 (p0) REVERT: E 154 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8372 (tm-30) REVERT: E 177 GLN cc_start: 0.8268 (tt0) cc_final: 0.7937 (pm20) REVERT: F 175 ASP cc_start: 0.8703 (p0) cc_final: 0.8034 (p0) REVERT: B 300 LYS cc_start: 0.8955 (mttm) cc_final: 0.8580 (mmmt) REVERT: B 413 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6928 (mm-30) REVERT: B 422 TYR cc_start: 0.8163 (t80) cc_final: 0.7454 (t80) REVERT: B 439 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7848 (mtp85) REVERT: B 456 MET cc_start: 0.9012 (ttp) cc_final: 0.8604 (tmm) REVERT: B 561 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 613 ARG cc_start: 0.8850 (mmm160) cc_final: 0.8596 (mmm-85) REVERT: C 77 GLN cc_start: 0.8433 (pm20) cc_final: 0.7844 (pm20) REVERT: C 89 ASP cc_start: 0.8905 (m-30) cc_final: 0.8417 (m-30) REVERT: C 110 GLN cc_start: 0.7998 (pm20) cc_final: 0.7796 (pm20) REVERT: C 164 LEU cc_start: 0.8288 (mp) cc_final: 0.7939 (tp) REVERT: D 4 MET cc_start: 0.8485 (mmp) cc_final: 0.8189 (mmp) REVERT: D 48 GLN cc_start: 0.8505 (mp10) cc_final: 0.8151 (mp10) REVERT: D 190 ASP cc_start: 0.7936 (t0) cc_final: 0.7646 (t70) outliers start: 1 outliers final: 1 residues processed: 184 average time/residue: 0.2297 time to fit residues: 57.8085 Evaluate side-chains 132 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.0060 chunk 54 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS C 169 HIS ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10033 Z= 0.338 Angle : 0.742 9.298 13667 Z= 0.372 Chirality : 0.048 0.320 1572 Planarity : 0.005 0.096 1746 Dihedral : 7.433 51.271 1469 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.26 % 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 (0.23), residues: 1197 helix: -1.92 (0.37), residues: 141 sheet: -1.63 (0.24), residues: 420 loop : -2.15 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 194 HIS 0.007 0.002 HIS B 538 PHE 0.025 0.002 PHE B 544 TYR 0.024 0.002 TYR F 97 ARG 0.007 0.001 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7965 (mm-30) REVERT: E 89 ASP cc_start: 0.8166 (m-30) cc_final: 0.5951 (p0) REVERT: E 154 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8318 (tm-30) REVERT: E 177 GLN cc_start: 0.8235 (tt0) cc_final: 0.8024 (pm20) REVERT: F 175 ASP cc_start: 0.8817 (p0) cc_final: 0.8080 (p0) REVERT: B 300 LYS cc_start: 0.8957 (mttm) cc_final: 0.8693 (mmmt) REVERT: B 413 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6902 (mm-30) REVERT: B 422 TYR cc_start: 0.8209 (t80) cc_final: 0.7837 (t80) REVERT: B 439 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7783 (mtp85) REVERT: B 456 MET cc_start: 0.8876 (ttp) cc_final: 0.8572 (tmm) REVERT: B 534 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7796 (mmm160) REVERT: B 561 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7512 (mm-30) REVERT: B 613 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8509 (mmm-85) REVERT: C 77 GLN cc_start: 0.8677 (pm20) cc_final: 0.8009 (pm20) REVERT: C 89 ASP cc_start: 0.9039 (m-30) cc_final: 0.8772 (m-30) REVERT: C 164 LEU cc_start: 0.8261 (mp) cc_final: 0.7938 (tp) REVERT: D 4 MET cc_start: 0.8551 (mmp) cc_final: 0.8288 (mmp) REVERT: D 42 TYR cc_start: 0.8932 (m-80) cc_final: 0.8693 (m-80) REVERT: D 48 GLN cc_start: 0.8501 (mp10) cc_final: 0.8166 (mp10) REVERT: D 87 GLU cc_start: 0.7372 (pm20) cc_final: 0.6141 (mp0) REVERT: D 190 ASP cc_start: 0.7982 (t0) cc_final: 0.7665 (t70) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2309 time to fit residues: 55.2502 Evaluate side-chains 134 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 109 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10033 Z= 0.171 Angle : 0.632 8.230 13667 Z= 0.313 Chirality : 0.045 0.264 1572 Planarity : 0.005 0.086 1746 Dihedral : 6.678 50.739 1469 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.09 % Allowed : 2.81 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -2.51 (0.24), residues: 1197 helix: -1.31 (0.41), residues: 140 sheet: -1.52 (0.24), residues: 426 loop : -1.81 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 219 HIS 0.007 0.001 HIS C 204 PHE 0.013 0.001 PHE D 141 TYR 0.016 0.001 TYR F 97 ARG 0.004 0.000 ARG C 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.7854 (m100) cc_final: 0.6739 (m100) REVERT: E 46 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7793 (mm-30) REVERT: E 89 ASP cc_start: 0.8050 (m-30) cc_final: 0.6112 (p0) REVERT: E 94 TYR cc_start: 0.7337 (p90) cc_final: 0.6935 (p90) REVERT: E 154 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8302 (tm-30) REVERT: F 175 ASP cc_start: 0.8879 (p0) cc_final: 0.8128 (p0) REVERT: F 193 ARG cc_start: 0.7172 (mtm180) cc_final: 0.6739 (mtm180) REVERT: B 245 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8580 (ttmt) REVERT: B 413 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6905 (mm-30) REVERT: B 422 TYR cc_start: 0.7909 (t80) cc_final: 0.7589 (t80) REVERT: B 439 ARG cc_start: 0.7854 (mtp85) cc_final: 0.7605 (mtp85) REVERT: B 456 MET cc_start: 0.8782 (ttp) cc_final: 0.8550 (tmm) REVERT: B 471 GLU cc_start: 0.8754 (pm20) cc_final: 0.8277 (pm20) REVERT: B 472 ILE cc_start: 0.9428 (mt) cc_final: 0.9010 (mp) REVERT: B 561 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7536 (mm-30) REVERT: B 613 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8150 (mmm-85) REVERT: C 77 GLN cc_start: 0.8552 (pm20) cc_final: 0.7860 (pm20) REVERT: C 89 ASP cc_start: 0.8960 (m-30) cc_final: 0.8650 (m-30) REVERT: C 164 LEU cc_start: 0.8183 (mp) cc_final: 0.7835 (tp) REVERT: C 213 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7665 (tttm) REVERT: D 48 GLN cc_start: 0.8432 (mp10) cc_final: 0.8163 (mp10) REVERT: D 87 GLU cc_start: 0.7186 (pm20) cc_final: 0.6540 (mm-30) REVERT: D 198 TYR cc_start: 0.6696 (m-80) cc_final: 0.6392 (m-80) outliers start: 1 outliers final: 0 residues processed: 197 average time/residue: 0.2301 time to fit residues: 62.1980 Evaluate side-chains 150 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 0.0030 chunk 71 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 8.9990 chunk 56 optimal weight: 0.0570 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10033 Z= 0.239 Angle : 0.660 9.083 13667 Z= 0.328 Chirality : 0.045 0.224 1572 Planarity : 0.005 0.094 1746 Dihedral : 6.547 49.821 1469 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -2.39 (0.24), residues: 1197 helix: -1.08 (0.42), residues: 140 sheet: -1.41 (0.25), residues: 425 loop : -1.79 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 36 HIS 0.004 0.001 HIS D 195 PHE 0.018 0.002 PHE B 544 TYR 0.013 0.002 TYR F 97 ARG 0.006 0.001 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.7939 (m100) cc_final: 0.6744 (m100) REVERT: E 46 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7832 (mm-30) REVERT: E 89 ASP cc_start: 0.8051 (m-30) cc_final: 0.6183 (p0) REVERT: E 94 TYR cc_start: 0.7751 (p90) cc_final: 0.7328 (p90) REVERT: E 154 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 175 ASP cc_start: 0.8856 (p0) cc_final: 0.8060 (p0) REVERT: F 193 ARG cc_start: 0.6988 (mtm180) cc_final: 0.6618 (mtm180) REVERT: B 245 LYS cc_start: 0.8901 (mtmt) cc_final: 0.8643 (ttmt) REVERT: B 300 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8607 (mtmt) REVERT: B 387 GLN cc_start: 0.9019 (tp40) cc_final: 0.8759 (tp40) REVERT: B 413 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6780 (mm-30) REVERT: B 422 TYR cc_start: 0.8031 (t80) cc_final: 0.7783 (t80) REVERT: B 439 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7694 (mtp85) REVERT: B 456 MET cc_start: 0.8776 (ttp) cc_final: 0.8528 (tmm) REVERT: B 471 GLU cc_start: 0.8536 (pm20) cc_final: 0.8095 (pm20) REVERT: B 472 ILE cc_start: 0.9584 (mt) cc_final: 0.9177 (mp) REVERT: B 561 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 613 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8212 (mmm-85) REVERT: C 77 GLN cc_start: 0.8543 (pm20) cc_final: 0.7775 (pm20) REVERT: C 89 ASP cc_start: 0.8992 (m-30) cc_final: 0.8658 (m-30) REVERT: C 164 LEU cc_start: 0.8222 (mp) cc_final: 0.7869 (tp) REVERT: C 182 LEU cc_start: 0.8610 (pp) cc_final: 0.8286 (pp) REVERT: C 213 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7697 (tttm) REVERT: D 4 MET cc_start: 0.8380 (mmp) cc_final: 0.8083 (mmp) REVERT: D 48 GLN cc_start: 0.8451 (mp10) cc_final: 0.8190 (mp10) REVERT: D 87 GLU cc_start: 0.7480 (pm20) cc_final: 0.6520 (mm-30) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2316 time to fit residues: 56.3014 Evaluate side-chains 145 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.0010 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 0.0170 overall best weight: 0.7226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10033 Z= 0.181 Angle : 0.626 8.809 13667 Z= 0.309 Chirality : 0.044 0.224 1572 Planarity : 0.005 0.088 1746 Dihedral : 6.162 50.226 1469 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.24), residues: 1197 helix: -0.87 (0.43), residues: 140 sheet: -1.28 (0.25), residues: 422 loop : -1.67 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 219 HIS 0.003 0.001 HIS B 265 PHE 0.016 0.001 PHE B 563 TYR 0.011 0.002 TYR F 42 ARG 0.005 0.000 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.7910 (m100) cc_final: 0.6947 (m100) REVERT: E 46 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7313 (mm-30) REVERT: E 94 TYR cc_start: 0.7674 (p90) cc_final: 0.7302 (p90) REVERT: E 154 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8312 (tm-30) REVERT: E 170 HIS cc_start: 0.9010 (m90) cc_final: 0.8791 (m170) REVERT: F 175 ASP cc_start: 0.8828 (p0) cc_final: 0.7977 (p0) REVERT: F 193 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6397 (mtm180) REVERT: B 245 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8730 (ttmt) REVERT: B 300 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8534 (mtmt) REVERT: B 413 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6781 (mm-30) REVERT: B 439 ARG cc_start: 0.7832 (mtp85) cc_final: 0.7616 (mtp85) REVERT: B 456 MET cc_start: 0.8746 (ttp) cc_final: 0.8481 (tmm) REVERT: B 471 GLU cc_start: 0.8776 (pm20) cc_final: 0.8429 (pm20) REVERT: B 561 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7295 (mm-30) REVERT: B 579 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7380 (tm-30) REVERT: B 613 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8148 (mmm-85) REVERT: C 3 GLN cc_start: 0.7734 (mt0) cc_final: 0.7270 (mt0) REVERT: C 77 GLN cc_start: 0.8488 (pm20) cc_final: 0.7838 (pm20) REVERT: C 89 ASP cc_start: 0.8873 (m-30) cc_final: 0.8464 (m-30) REVERT: C 148 LYS cc_start: 0.7941 (tttp) cc_final: 0.7712 (tppt) REVERT: C 164 LEU cc_start: 0.8244 (mp) cc_final: 0.7882 (tp) REVERT: C 201 ASN cc_start: 0.4974 (m110) cc_final: 0.4066 (m110) REVERT: C 213 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7740 (tttm) REVERT: D 4 MET cc_start: 0.8440 (mmp) cc_final: 0.8225 (mmp) REVERT: D 48 GLN cc_start: 0.8450 (mp10) cc_final: 0.8199 (mp10) REVERT: D 68 PHE cc_start: 0.7426 (m-80) cc_final: 0.7179 (m-80) REVERT: D 87 GLU cc_start: 0.7388 (pm20) cc_final: 0.6596 (mm-30) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2209 time to fit residues: 56.7486 Evaluate side-chains 143 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.0470 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 0.0010 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.1888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 HIS ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10033 Z= 0.224 Angle : 0.647 9.321 13667 Z= 0.319 Chirality : 0.045 0.230 1572 Planarity : 0.005 0.091 1746 Dihedral : 6.208 49.660 1469 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.13 (0.24), residues: 1197 helix: -0.79 (0.43), residues: 140 sheet: -1.29 (0.25), residues: 419 loop : -1.59 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 219 HIS 0.004 0.001 HIS D 204 PHE 0.016 0.002 PHE B 544 TYR 0.012 0.002 TYR E 108 ARG 0.004 0.000 ARG E 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.7920 (m100) cc_final: 0.6993 (m100) REVERT: E 46 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7600 (mm-30) REVERT: E 94 TYR cc_start: 0.7820 (p90) cc_final: 0.7511 (p90) REVERT: E 154 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8386 (tm-30) REVERT: F 180 MET cc_start: 0.8956 (tpt) cc_final: 0.8500 (tpt) REVERT: F 193 ARG cc_start: 0.7002 (mtm180) cc_final: 0.6738 (mtm180) REVERT: B 245 LYS cc_start: 0.9016 (mtmt) cc_final: 0.8711 (ttmt) REVERT: B 300 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8762 (mmmm) REVERT: B 413 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6819 (mm-30) REVERT: B 422 TYR cc_start: 0.7951 (t80) cc_final: 0.7678 (t80) REVERT: B 439 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7657 (mtp85) REVERT: B 456 MET cc_start: 0.8823 (ttp) cc_final: 0.8454 (tmm) REVERT: B 471 GLU cc_start: 0.8621 (pm20) cc_final: 0.8356 (pm20) REVERT: B 561 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 579 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7407 (tm-30) REVERT: B 613 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8186 (mmm-85) REVERT: C 3 GLN cc_start: 0.7847 (mt0) cc_final: 0.7422 (mt0) REVERT: C 67 LEU cc_start: 0.7663 (pp) cc_final: 0.7461 (pp) REVERT: C 77 GLN cc_start: 0.8548 (pm20) cc_final: 0.7824 (pm20) REVERT: C 86 GLN cc_start: 0.8889 (tm-30) cc_final: 0.8243 (tm-30) REVERT: C 89 ASP cc_start: 0.9014 (m-30) cc_final: 0.8537 (m-30) REVERT: C 164 LEU cc_start: 0.8268 (mp) cc_final: 0.7899 (tp) REVERT: C 213 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7742 (tttm) REVERT: D 4 MET cc_start: 0.8472 (mmp) cc_final: 0.8236 (mmp) REVERT: D 48 GLN cc_start: 0.8470 (mp10) cc_final: 0.8237 (mp10) REVERT: D 68 PHE cc_start: 0.7441 (m-80) cc_final: 0.7200 (m-80) REVERT: D 87 GLU cc_start: 0.7391 (pm20) cc_final: 0.6393 (mm-30) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2339 time to fit residues: 56.2732 Evaluate side-chains 137 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10033 Z= 0.291 Angle : 0.682 9.636 13667 Z= 0.339 Chirality : 0.046 0.267 1572 Planarity : 0.005 0.090 1746 Dihedral : 6.433 55.264 1469 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.15 (0.24), residues: 1197 helix: -0.87 (0.43), residues: 138 sheet: -1.37 (0.25), residues: 399 loop : -1.55 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 219 HIS 0.004 0.001 HIS D 195 PHE 0.023 0.002 PHE B 544 TYR 0.016 0.002 TYR E 108 ARG 0.005 0.001 ARG B 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8468 (tm-30) REVERT: F 180 MET cc_start: 0.9070 (tpt) cc_final: 0.8615 (tpt) REVERT: F 193 ARG cc_start: 0.7087 (mtm180) cc_final: 0.6832 (mtm180) REVERT: B 245 LYS cc_start: 0.8999 (mtmt) cc_final: 0.8682 (ttmt) REVERT: B 300 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8772 (mmmm) REVERT: B 413 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6895 (mm-30) REVERT: B 422 TYR cc_start: 0.8037 (t80) cc_final: 0.7800 (t80) REVERT: B 439 ARG cc_start: 0.7938 (mtp85) cc_final: 0.7728 (mtp85) REVERT: B 456 MET cc_start: 0.8923 (ttp) cc_final: 0.8533 (tmm) REVERT: B 561 GLU cc_start: 0.7999 (mm-30) cc_final: 0.7456 (mm-30) REVERT: B 579 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7408 (tm-30) REVERT: B 613 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8274 (mmm-85) REVERT: C 3 GLN cc_start: 0.7408 (mt0) cc_final: 0.6896 (mt0) REVERT: C 77 GLN cc_start: 0.8662 (pm20) cc_final: 0.7941 (pm20) REVERT: C 89 ASP cc_start: 0.9016 (m-30) cc_final: 0.8313 (m-30) REVERT: C 164 LEU cc_start: 0.8285 (mp) cc_final: 0.7917 (tp) REVERT: C 213 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7734 (tttm) REVERT: D 4 MET cc_start: 0.8404 (mmp) cc_final: 0.8155 (mmp) REVERT: D 48 GLN cc_start: 0.8437 (mp10) cc_final: 0.8190 (mp10) REVERT: D 87 GLU cc_start: 0.7395 (pm20) cc_final: 0.6381 (mm-30) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2216 time to fit residues: 50.9401 Evaluate side-chains 126 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.3980 chunk 106 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10033 Z= 0.179 Angle : 0.640 8.977 13667 Z= 0.315 Chirality : 0.045 0.284 1572 Planarity : 0.005 0.088 1746 Dihedral : 6.205 52.615 1469 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -1.97 (0.24), residues: 1197 helix: -0.51 (0.45), residues: 133 sheet: -1.24 (0.25), residues: 413 loop : -1.48 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 219 HIS 0.004 0.001 HIS F 203 PHE 0.012 0.002 PHE B 458 TYR 0.012 0.001 TYR E 100 ARG 0.004 0.000 ARG E 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2394 Ramachandran restraints generated. 1197 Oldfield, 0 Emsley, 1197 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 TRP cc_start: 0.7866 (m100) cc_final: 0.6916 (m100) REVERT: E 46 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7456 (mm-30) REVERT: E 94 TYR cc_start: 0.7678 (p90) cc_final: 0.7381 (p90) REVERT: E 105 TRP cc_start: 0.7097 (m-90) cc_final: 0.6832 (m-90) REVERT: E 154 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8370 (tm-30) REVERT: F 180 MET cc_start: 0.9050 (tpt) cc_final: 0.8717 (tpt) REVERT: F 193 ARG cc_start: 0.7048 (mtm180) cc_final: 0.6774 (mtm180) REVERT: B 245 LYS cc_start: 0.8956 (mtmt) cc_final: 0.8647 (ttmt) REVERT: B 300 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8684 (mmmm) REVERT: B 413 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 439 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7596 (mtp85) REVERT: B 456 MET cc_start: 0.8794 (ttp) cc_final: 0.8401 (tmm) REVERT: B 471 GLU cc_start: 0.8616 (pm20) cc_final: 0.8274 (pm20) REVERT: B 561 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 579 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 613 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8122 (mmm-85) REVERT: C 3 GLN cc_start: 0.7332 (mt0) cc_final: 0.6972 (mt0) REVERT: C 67 LEU cc_start: 0.7599 (pp) cc_final: 0.7357 (pp) REVERT: C 77 GLN cc_start: 0.8576 (pm20) cc_final: 0.7894 (pm20) REVERT: C 89 ASP cc_start: 0.8963 (m-30) cc_final: 0.8297 (m-30) REVERT: C 164 LEU cc_start: 0.8257 (mp) cc_final: 0.7876 (tp) REVERT: C 182 LEU cc_start: 0.8833 (pp) cc_final: 0.8565 (pp) REVERT: C 210 LYS cc_start: 0.7663 (tptp) cc_final: 0.7449 (tptp) REVERT: C 213 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7787 (tttm) REVERT: D 4 MET cc_start: 0.8527 (mmp) cc_final: 0.8326 (mmp) REVERT: D 48 GLN cc_start: 0.8377 (mp10) cc_final: 0.8060 (mp10) REVERT: D 87 GLU cc_start: 0.7322 (pm20) cc_final: 0.6257 (mm-30) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2277 time to fit residues: 54.5519 Evaluate side-chains 137 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 100 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.099516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080282 restraints weight = 27916.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.082343 restraints weight = 18299.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.083786 restraints weight = 13477.773| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 10033 Z= 0.471 Angle : 0.840 10.470 13667 Z= 0.418 Chirality : 0.051 0.243 1572 Planarity : 0.006 0.096 1746 Dihedral : 7.080 57.361 1469 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.24), residues: 1197 helix: -1.37 (0.40), residues: 136 sheet: -1.53 (0.26), residues: 382 loop : -1.73 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 433 HIS 0.007 0.002 HIS E 35 PHE 0.037 0.003 PHE B 544 TYR 0.021 0.003 TYR E 108 ARG 0.006 0.001 ARG B 530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.87 seconds wall clock time: 38 minutes 44.47 seconds (2324.47 seconds total)