Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:21:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/04_2023/6jmr_9850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/04_2023/6jmr_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_9850/04_2023/6jmr_9850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/04_2023/6jmr_9850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/04_2023/6jmr_9850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/04_2023/6jmr_9850_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-1.21rc1-4938/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 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 chiralities: 3 Time building chain proxies: 5.50, per 1000 atoms: 0.56 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: 3.87 Conformation dependent library (CDL) restraints added in 1.6 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: 0.99 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: 2.79 Time building geometry restraints manager: 4.14 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: 5187 15.59 - 31.18: 641 31.18 - 46.77: 112 46.77 - 62.36: 18 62.36 - 77.95: 9 Dihedral angle restraints: 5967 sinusoidal: 2248 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 5964 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.740 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- 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 : 14.047 77.952 3545 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 % 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 *********************** 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 : 1.096 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 outliers start: 6 outliers final: 3 residues processed: 247 average time/residue: 0.2683 time to fit residues: 89.1202 Evaluate side-chains 141 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0904 time to fit residues: 2.0008 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 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** D 43 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 10033 Z= 0.215 Angle : 0.712 10.671 13667 Z= 0.361 Chirality : 0.046 0.217 1572 Planarity : 0.006 0.103 1746 Dihedral : 6.476 45.092 1364 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.00 % 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: -3.24 (0.22), residues: 1197 helix: -2.35 (0.36), residues: 139 sheet: -1.78 (0.22), residues: 450 loop : -2.35 (0.22), residues: 608 *********************** 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 216 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.160 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 outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2374 time to fit residues: 70.5099 Evaluate side-chains 143 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.138 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5231 ------------------------------------------------------------------------------- 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: 4.9990 chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 10033 Z= 0.381 Angle : 0.771 9.486 13667 Z= 0.389 Chirality : 0.048 0.215 1572 Planarity : 0.006 0.103 1746 Dihedral : 6.535 41.696 1364 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer Outliers : 0.00 % 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: -3.04 (0.22), residues: 1197 helix: -2.14 (0.36), residues: 145 sheet: -1.63 (0.24), residues: 412 loop : -2.26 (0.23), residues: 640 *********************** 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 191 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.142 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 outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2425 time to fit residues: 63.6667 Evaluate side-chains 124 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6249 ------------------------------------------------------------------------------- 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: 0.9980 chunk 86 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 121 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** D 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 10033 Z= 0.286 Angle : 0.707 9.015 13667 Z= 0.353 Chirality : 0.047 0.230 1572 Planarity : 0.005 0.095 1746 Dihedral : 6.153 40.605 1364 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer Outliers : 0.09 % 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: -2.88 (0.23), residues: 1197 helix: -1.77 (0.38), residues: 140 sheet: -1.60 (0.24), residues: 415 loop : -2.15 (0.23), residues: 642 *********************** 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 185 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.179 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 outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.2201 time to fit residues: 57.9289 Evaluate side-chains 134 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0941 time to fit residues: 1.7099 ------------------------------------------------------------------------------- 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: 2.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 62 optimal weight: 0.0470 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10033 Z= 0.221 Angle : 0.656 8.866 13667 Z= 0.326 Chirality : 0.045 0.233 1572 Planarity : 0.005 0.091 1746 Dihedral : 5.766 40.030 1364 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer Outliers : 0.00 % 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: -2.63 (0.23), residues: 1197 helix: -1.37 (0.40), residues: 140 sheet: -1.53 (0.24), residues: 426 loop : -1.96 (0.24), residues: 631 *********************** 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 194 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.236 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 outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2135 time to fit residues: 58.7885 Evaluate side-chains 135 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5981 ------------------------------------------------------------------------------- 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: 8.9990 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10033 Z= 0.211 Angle : 0.646 9.352 13667 Z= 0.322 Chirality : 0.045 0.216 1572 Planarity : 0.005 0.090 1746 Dihedral : 5.577 40.756 1364 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 0.00 % 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: -2.43 (0.24), residues: 1197 helix: -1.12 (0.41), residues: 140 sheet: -1.38 (0.24), residues: 429 loop : -1.86 (0.25), residues: 628 *********************** 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 184 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.157 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 outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2206 time to fit residues: 57.5122 Evaluate side-chains 136 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5043 ------------------------------------------------------------------------------- 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: 0.9990 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10033 Z= 0.223 Angle : 0.655 9.491 13667 Z= 0.323 Chirality : 0.045 0.228 1572 Planarity : 0.005 0.091 1746 Dihedral : 5.517 39.872 1364 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.00 % 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: -2.33 (0.24), residues: 1197 helix: -1.00 (0.42), residues: 140 sheet: -1.35 (0.25), residues: 428 loop : -1.78 (0.25), residues: 629 *********************** 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 172 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.218 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 outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2250 time to fit residues: 55.6896 Evaluate side-chains 135 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5732 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** B 542 HIS B 556 HIS ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 10033 Z= 0.201 Angle : 0.657 9.645 13667 Z= 0.322 Chirality : 0.045 0.219 1572 Planarity : 0.005 0.089 1746 Dihedral : 5.432 39.691 1364 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer Outliers : 0.00 % 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: -2.25 (0.24), residues: 1197 helix: -0.87 (0.42), residues: 140 sheet: -1.35 (0.25), residues: 417 loop : -1.69 (0.25), residues: 640 *********************** 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 178 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.199 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 outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2250 time to fit residues: 56.6943 Evaluate side-chains 129 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6038 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 0.0570 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.6904 ------------------------------------------------------------------------------- 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** C 169 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10033 Z= 0.277 Angle : 0.695 10.152 13667 Z= 0.345 Chirality : 0.046 0.259 1572 Planarity : 0.005 0.092 1746 Dihedral : 5.621 39.337 1364 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 0.00 % 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: -2.30 (0.24), residues: 1197 helix: -0.98 (0.42), residues: 140 sheet: -1.38 (0.25), residues: 406 loop : -1.72 (0.25), residues: 651 *********************** 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 158 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2170 time to fit residues: 48.8495 Evaluate side-chains 116 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5919 ------------------------------------------------------------------------------- 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: 2.9990 chunk 56 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10033 Z= 0.225 Angle : 0.672 9.732 13667 Z= 0.332 Chirality : 0.046 0.265 1572 Planarity : 0.005 0.088 1746 Dihedral : 5.534 39.423 1364 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % 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: -2.16 (0.24), residues: 1197 helix: -0.72 (0.43), residues: 134 sheet: -1.38 (0.25), residues: 417 loop : -1.59 (0.25), residues: 646 ********************** 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 157 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2189 time to fit residues: 49.0151 Evaluate side-chains 120 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5726 ------------------------------------------------------------------------------- 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: 1.9990 chunk 92 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 95 GLN ** B 267 ASN ** 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 = 0.3650 r_free = 0.3650 target = 0.102483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.083549 restraints weight = 27493.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.085707 restraints weight = 17596.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087244 restraints weight = 12835.867| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 10033 Z= 0.318 Angle : 0.719 10.285 13667 Z= 0.357 Chirality : 0.047 0.250 1572 Planarity : 0.005 0.092 1746 Dihedral : 5.701 39.050 1364 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.00 % 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: -2.29 (0.24), residues: 1197 helix: -1.03 (0.41), residues: 141 sheet: -1.39 (0.25), residues: 415 loop : -1.69 (0.25), residues: 641 =============================================================================== Job complete usr+sys time: 2024.16 seconds wall clock time: 37 minutes 52.42 seconds (2272.42 seconds total)