Starting phenix.real_space_refine (version: dev) on Sun Feb 19 09:38:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/02_2023/6jmr_9850_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/02_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_9850/02_2023/6jmr_9850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/02_2023/6jmr_9850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/02_2023/6jmr_9850_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jmr_9850/02_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 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-4877/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: 5.92, per 1000 atoms: 0.60 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: 3.76 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: 1.05 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: 2.83 Time building geometry restraints manager: 4.22 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=" 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 bond pdb=" C SER F 7 " pdb=" N PRO F 8 " ideal model delta sigma weight residual 1.333 1.364 -0.031 1.20e-02 6.94e+03 6.54e+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: 5216 15.59 - 31.18: 642 31.18 - 46.77: 112 46.77 - 62.36: 18 62.36 - 77.95: 9 Dihedral angle restraints: 5997 sinusoidal: 2278 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 5994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1210 0.061 - 0.122: 304 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 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. 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: 0.250 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: 2.290 Check model and map are aligned: 0.150 Process input model: 28.860 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 10033 Z= 0.419 Angle : 1.053 11.251 13667 Z= 0.593 Chirality : 0.056 0.306 1572 Planarity : 0.008 0.129 1746 Dihedral : 14.008 77.952 3575 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 : 1.146 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: 0.2640 time to fit residues: 86.9989 Evaluate side-chains 141 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0881 time to fit residues: 1.9117 ------------------------------------------------------------------------------- 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: 0.7758 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10033 Z= 0.222 Angle : 0.706 10.022 13667 Z= 0.360 Chirality : 0.045 0.256 1572 Planarity : 0.006 0.104 1746 Dihedral : 6.504 45.324 1394 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.83 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: -2.36 (0.36), residues: 139 sheet: -1.78 (0.22), residues: 450 loop : -2.36 (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 : 1.154 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: 0 outliers final: 0 residues processed: 216 average time/residue: 0.2372 time to fit residues: 70.2965 Evaluate side-chains 141 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6253 ------------------------------------------------------------------------------- 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: 0.9990 chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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: 0.7844 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 10033 Z= 0.349 Angle : 0.742 9.255 13667 Z= 0.377 Chirality : 0.048 0.222 1572 Planarity : 0.006 0.102 1746 Dihedral : 6.470 41.563 1394 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % 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: -3.01 (0.22), residues: 1197 helix: -2.10 (0.37), residues: 145 sheet: -1.61 (0.24), residues: 409 loop : -2.23 (0.23), residues: 643 *********************** 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 190 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.070 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: 190 average time/residue: 0.2412 time to fit residues: 62.9929 Evaluate side-chains 125 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.268 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6944 ------------------------------------------------------------------------------- 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: 0.7980 chunk 86 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 34 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: 0.7847 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 10033 Z= 0.312 Angle : 0.718 10.089 13667 Z= 0.362 Chirality : 0.047 0.354 1572 Planarity : 0.005 0.098 1746 Dihedral : 6.291 40.903 1394 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer Outliers : 0.19 % 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: -2.85 (0.23), residues: 1197 helix: -1.76 (0.38), residues: 140 sheet: -1.51 (0.24), residues: 414 loop : -2.19 (0.23), residues: 643 *********************** 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 176 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 176 average time/residue: 0.2254 time to fit residues: 56.0093 Evaluate side-chains 132 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0946 time to fit residues: 1.7792 ------------------------------------------------------------------------------- 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: 3.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 10033 Z= 0.264 Angle : 0.682 9.584 13667 Z= 0.341 Chirality : 0.046 0.251 1572 Planarity : 0.005 0.091 1746 Dihedral : 6.008 41.008 1394 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % 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: -2.72 (0.23), residues: 1197 helix: -1.52 (0.40), residues: 140 sheet: -1.58 (0.24), residues: 432 loop : -2.01 (0.24), residues: 625 *********************** 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 174 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.150 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: 174 average time/residue: 0.2112 time to fit residues: 52.4472 Evaluate side-chains 128 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.113 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5734 ------------------------------------------------------------------------------- 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: 6.9990 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 121 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9524 ------------------------------------------------------------------------------- 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 34 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: 0.7798 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 10033 Z= 0.202 Angle : 0.644 9.560 13667 Z= 0.321 Chirality : 0.045 0.226 1572 Planarity : 0.005 0.091 1746 Dihedral : 5.708 40.241 1394 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.40 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 : 0.09 % 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: -2.47 (0.24), residues: 1197 helix: -1.17 (0.41), residues: 140 sheet: -1.46 (0.24), residues: 429 loop : -1.84 (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 186 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.289 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: 186 average time/residue: 0.2177 time to fit residues: 57.9334 Evaluate side-chains 126 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.205 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6642 ------------------------------------------------------------------------------- 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: 0.2980 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.2980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 34 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: 0.7757 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 10033 Z= 0.171 Angle : 0.630 9.890 13667 Z= 0.312 Chirality : 0.044 0.213 1572 Planarity : 0.005 0.090 1746 Dihedral : 5.394 39.626 1394 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % 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: -2.25 (0.24), residues: 1197 helix: -0.85 (0.43), residues: 138 sheet: -1.26 (0.25), residues: 417 loop : -1.77 (0.24), residues: 642 *********************** 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 183 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.184 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: 183 average time/residue: 0.2009 time to fit residues: 53.6147 Evaluate side-chains 132 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5004 ------------------------------------------------------------------------------- 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: 5.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 95 optimal weight: 0.0870 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- 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 34 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** B 542 HIS B 556 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 10033 Z= 0.269 Angle : 0.678 10.400 13667 Z= 0.338 Chirality : 0.045 0.209 1572 Planarity : 0.005 0.091 1746 Dihedral : 5.639 39.074 1394 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % 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: -0.83 (0.42), residues: 139 sheet: -1.27 (0.25), residues: 411 loop : -1.78 (0.24), residues: 647 *********************** 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 170 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.198 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: 170 average time/residue: 0.2136 time to fit residues: 52.6100 Evaluate side-chains 120 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5085 ------------------------------------------------------------------------------- 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: 0.0170 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4144 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= 0.189 Angle : 0.643 10.334 13667 Z= 0.318 Chirality : 0.045 0.224 1572 Planarity : 0.005 0.088 1746 Dihedral : 5.427 39.230 1394 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % Twisted General : 0.09 % 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: -2.09 (0.24), residues: 1197 helix: -0.62 (0.43), residues: 135 sheet: -1.20 (0.25), residues: 414 loop : -1.66 (0.25), residues: 648 *********************** 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 179 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.036 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: 179 average time/residue: 0.2172 time to fit residues: 54.9907 Evaluate side-chains 129 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.160 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6727 ------------------------------------------------------------------------------- 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: 0.7980 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.4980 chunk 115 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 0.0770 chunk 106 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 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: 0.7755 moved from start: 0.4341 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= 0.178 Angle : 0.646 9.965 13667 Z= 0.319 Chirality : 0.045 0.270 1572 Planarity : 0.005 0.090 1746 Dihedral : 5.354 38.414 1394 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.51 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 : 0.09 % 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: -2.00 (0.24), residues: 1197 helix: -0.46 (0.44), residues: 133 sheet: -1.15 (0.25), residues: 416 loop : -1.62 (0.25), residues: 648 ********************** 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 182 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.039 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: 182 average time/residue: 0.2163 time to fit residues: 56.3554 Evaluate side-chains 125 residues out of total 1068 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 1.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6561 ------------------------------------------------------------------------------- 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: 0.9980 chunk 92 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 0.0050 chunk 87 optimal weight: 4.9990 chunk 5 optimal weight: 0.0980 overall best weight: 1.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 13 GLN ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 GLN ** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.103928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.084947 restraints weight = 27592.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087113 restraints weight = 17555.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.088635 restraints weight = 12783.963| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 10033 Z= 0.293 Angle : 0.697 10.627 13667 Z= 0.347 Chirality : 0.046 0.274 1572 Planarity : 0.005 0.090 1746 Dihedral : 5.559 38.390 1394 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % 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: -2.07 (0.24), residues: 1197 helix: -0.36 (0.46), residues: 126 sheet: -1.31 (0.25), residues: 421 loop : -1.59 (0.25), residues: 650 =============================================================================== Job complete usr+sys time: 2017.49 seconds wall clock time: 37 minutes 57.30 seconds (2277.30 seconds total)