Starting phenix.real_space_refine (version: dev) on Mon Dec 12 08:24:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/12_2022/6wwu_21948_updated.pdb" } resolution = 2.7 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 39": "OD1" <-> "OD2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ASP 438": "OD1" <-> "OD2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B GLU 123": "OE1" <-> "OE2" Residue "B ASP 128": "OD1" <-> "OD2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 390": "NH1" <-> "NH2" Residue "K ARG 399": "NH1" <-> "NH2" Residue "K ARG 406": "NH1" <-> "NH2" Residue "K GLU 410": "OE1" <-> "OE2" Residue "K GLU 447": "OE1" <-> "OE2" Residue "K GLU 460": "OE1" <-> "OE2" Residue "K ASP 468": "OD1" <-> "OD2" Residue "K ARG 469": "NH1" <-> "NH2" Residue "K GLU 472": "OE1" <-> "OE2" Residue "K TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 520": "OE1" <-> "OE2" Residue "K GLU 535": "OE1" <-> "OE2" Residue "K ARG 550": "NH1" <-> "NH2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 579": "OD1" <-> "OD2" Residue "K ASP 638": "OD1" <-> "OD2" Residue "K GLU 722": "OE1" <-> "OE2" Residue "K ARG 728": "NH1" <-> "NH2" Residue "K TYR 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9688 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3449 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Conformer: "B" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} bond proxies already assigned to first conformer: 3501 Chain: "B" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3389 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 410} Chain: "K" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2700 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 11, 'TRANS': 333} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'GDP': 1, 'TA1': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 108 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 108 " occ=0.50 Time building chain proxies: 7.73, per 1000 atoms: 0.80 Number of scatterers: 9688 At special positions: 0 Unit cell: (73.959, 107.199, 113.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 62 16.00 P 7 15.00 Mg 1 11.99 O 1894 8.00 N 1649 7.00 C 6075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 1.9 seconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 9 sheets defined 37.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.732A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 42 No H-bonds generated for 'chain 'A' and resid 39 through 42' Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 127 Processing helix chain 'A' and resid 145 through 160 removed outlier: 4.546A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.757A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 removed outlier: 3.589A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.113A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.628A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 295 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.975A pdb=" N TRP A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 4.013A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.617A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 28 removed outlier: 4.249A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 removed outlier: 3.836A pdb=" N ILE B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASN B 48 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 49' Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.889A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 3.773A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.648A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.881A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 323 through 336 removed outlier: 4.019A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 390 removed outlier: 3.831A pdb=" N ARG B 380 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 removed outlier: 4.227A pdb=" N GLU B 410 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET B 415 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER B 420 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN B 424 " --> pdb=" O GLU B 421 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 425 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 455 through 462 removed outlier: 3.608A pdb=" N TYR K 459 " --> pdb=" O GLN K 455 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR K 461 " --> pdb=" O THR K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 470 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 501 through 513 removed outlier: 5.181A pdb=" N PHE K 510 " --> pdb=" O CYS K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 577 through 590 removed outlier: 3.893A pdb=" N SER K 582 " --> pdb=" O SER K 578 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS K 589 " --> pdb=" O GLU K 585 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN K 590 " --> pdb=" O LEU K 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 676 Processing helix chain 'K' and resid 692 through 696 Processing helix chain 'K' and resid 698 through 701 No H-bonds generated for 'chain 'K' and resid 698 through 701' Processing helix chain 'K' and resid 721 through 734 Processing sheet with id= A, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.785A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE A 171 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 317 through 321 Processing sheet with id= D, first strand: chain 'B' and resid 63 through 65 removed outlier: 8.592A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY B 132 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ILE B 7 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLN B 134 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS B 137 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE B 167 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.677A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 368 " --> pdb=" O ALA B 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 51 through 53 Processing sheet with id= F, first strand: chain 'B' and resid 316 through 318 removed outlier: 6.153A pdb=" N ALA B 352 " --> pdb=" O PHE B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'K' and resid 440 through 444 removed outlier: 3.894A pdb=" N VAL K 440 " --> pdb=" O VAL K 396 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR K 707 " --> pdb=" O THR K 395 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ALA K 397 " --> pdb=" O THR K 707 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET K 709 " --> pdb=" O ALA K 397 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ARG K 399 " --> pdb=" O MET K 709 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA K 711 " --> pdb=" O ARG K 399 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG K 401 " --> pdb=" O ALA K 711 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL K 713 " --> pdb=" O ARG K 401 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS K 628 " --> pdb=" O LYS K 617 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS K 617 " --> pdb=" O HIS K 628 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE K 609 " --> pdb=" O LEU K 636 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER K 528 " --> pdb=" O THR K 610 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 423 through 426 Processing sheet with id= I, first strand: chain 'K' and resid 556 through 559 315 hydrogen bonds defined for protein. 819 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1660 1.31 - 1.44: 2668 1.44 - 1.56: 5469 1.56 - 1.69: 9 1.69 - 1.81: 99 Bond restraints: 9905 Sorted by residual: bond pdb=" C22 TA1 B 502 " pdb=" O09 TA1 B 502 " ideal model delta sigma weight residual 1.335 1.455 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C27 TA1 B 502 " pdb=" O11 TA1 B 502 " ideal model delta sigma weight residual 1.329 1.446 -0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" C12 TA1 B 502 " pdb=" O04 TA1 B 502 " ideal model delta sigma weight residual 1.337 1.443 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C MET A 425 " pdb=" O MET A 425 " ideal model delta sigma weight residual 1.236 1.295 -0.059 1.22e-02 6.72e+03 2.34e+01 bond pdb=" C10 TA1 B 502 " pdb=" C18 TA1 B 502 " ideal model delta sigma weight residual 1.611 1.515 0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 9900 not shown) Histogram of bond angle deviations from ideal: 87.56 - 97.46: 4 97.46 - 107.37: 476 107.37 - 117.27: 6609 117.27 - 127.18: 6238 127.18 - 137.08: 128 Bond angle restraints: 13455 Sorted by residual: angle pdb=" N MET K 598 " pdb=" CA MET K 598 " pdb=" C MET K 598 " ideal model delta sigma weight residual 108.49 101.25 7.24 1.15e+00 7.56e-01 3.97e+01 angle pdb=" O LEU B 65 " pdb=" C LEU B 65 " pdb=" N VAL B 66 " ideal model delta sigma weight residual 123.27 130.63 -7.36 1.18e+00 7.18e-01 3.89e+01 angle pdb=" CA GLY B 269 " pdb=" C GLY B 269 " pdb=" N PHE B 270 " ideal model delta sigma weight residual 114.58 119.88 -5.30 8.60e-01 1.35e+00 3.80e+01 angle pdb=" CA LEU B 273 " pdb=" C LEU B 273 " pdb=" N THR B 274 " ideal model delta sigma weight residual 116.37 123.93 -7.56 1.23e+00 6.61e-01 3.78e+01 angle pdb=" C THR A 94 " pdb=" CA THR A 94 " pdb=" CB THR A 94 " ideal model delta sigma weight residual 110.42 122.23 -11.81 1.99e+00 2.53e-01 3.52e+01 ... (remaining 13450 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.13: 5699 33.13 - 66.25: 165 66.25 - 99.38: 11 99.38 - 132.50: 1 132.50 - 165.63: 3 Dihedral angle restraints: 5879 sinusoidal: 2358 harmonic: 3521 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -125.10 -165.63 1 2.00e+01 2.50e-03 4.72e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -43.65 148.24 1 2.00e+01 2.50e-03 4.44e+01 dihedral pdb=" O5' GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PA GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sinusoidal sigma weight residual 274.12 141.02 133.10 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 5876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1250 0.081 - 0.162: 193 0.162 - 0.243: 29 0.243 - 0.324: 4 0.324 - 0.405: 3 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA MET K 598 " pdb=" N MET K 598 " pdb=" C MET K 598 " pdb=" CB MET K 598 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" C18 TA1 B 502 " pdb=" C10 TA1 B 502 " pdb=" C17 TA1 B 502 " pdb=" C20 TA1 B 502 " both_signs ideal model delta sigma weight residual False -3.16 -2.76 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ILE A 114 " pdb=" N ILE A 114 " pdb=" C ILE A 114 " pdb=" CB ILE A 114 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.86e+00 ... (remaining 1476 not shown) Planarity restraints: 1740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 644 " -0.860 9.50e-02 1.11e+02 3.85e-01 9.02e+01 pdb=" NE ARG K 644 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG K 644 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG K 644 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 644 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 2 " -0.832 9.50e-02 1.11e+02 3.73e-01 8.45e+01 pdb=" NE ARG B 2 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B 2 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 2 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 2 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 422 " -0.702 9.50e-02 1.11e+02 3.14e-01 6.02e+01 pdb=" NE ARG A 422 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 422 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 422 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 422 " -0.023 2.00e-02 2.50e+03 ... (remaining 1737 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 165 2.64 - 3.20: 8687 3.20 - 3.77: 14461 3.77 - 4.33: 21234 4.33 - 4.90: 35283 Nonbonded interactions: 79830 Sorted by model distance: nonbonded pdb=" OH ATYR A 108 " pdb=" O SER K 650 " model vdw 2.072 2.440 nonbonded pdb=" O LEU B 192 " pdb=" OG1 THR B 196 " model vdw 2.077 2.440 nonbonded pdb=" OG SER A 241 " pdb=" O VAL A 250 " model vdw 2.152 2.440 nonbonded pdb=" O SER K 444 " pdb=" OG SER K 444 " model vdw 2.159 2.440 nonbonded pdb=" OG SER K 522 " pdb=" OG1 THR K 616 " model vdw 2.160 2.440 ... (remaining 79825 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6075 2.51 5 N 1649 2.21 5 O 1894 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.170 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 30.810 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.011 0.120 9905 Z= 0.707 Angle : 1.255 12.438 13455 Z= 0.788 Chirality : 0.064 0.405 1479 Planarity : 0.023 0.385 1740 Dihedral : 16.222 165.630 3621 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.79 % Favored : 93.97 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.20), residues: 1213 helix: -2.36 (0.20), residues: 476 sheet: -1.82 (0.31), residues: 217 loop : -3.20 (0.22), residues: 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 279 time to evaluate : 1.167 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 300 average time/residue: 1.0001 time to fit residues: 325.7194 Evaluate side-chains 220 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 210 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.1743 time to fit residues: 2.0307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 107 HIS A 197 HIS A 256 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 28 HIS ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 335 ASN K 393 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 9905 Z= 0.309 Angle : 0.641 7.179 13455 Z= 0.320 Chirality : 0.046 0.240 1479 Planarity : 0.006 0.069 1740 Dihedral : 9.950 154.425 1366 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.22), residues: 1213 helix: -1.04 (0.23), residues: 472 sheet: -1.02 (0.32), residues: 240 loop : -2.57 (0.25), residues: 501 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 238 average time/residue: 0.9496 time to fit residues: 246.8770 Evaluate side-chains 220 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 14 residues processed: 3 average time/residue: 0.5527 time to fit residues: 3.5200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 256 GLN B 15 GLN B 131 GLN B 291 GLN B 334 GLN K 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 9905 Z= 0.333 Angle : 0.615 6.731 13455 Z= 0.302 Chirality : 0.045 0.212 1479 Planarity : 0.005 0.054 1740 Dihedral : 9.624 149.003 1366 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.23), residues: 1213 helix: -0.49 (0.24), residues: 473 sheet: -0.55 (0.34), residues: 234 loop : -2.20 (0.25), residues: 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 225 time to evaluate : 1.179 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 26 residues processed: 247 average time/residue: 1.0944 time to fit residues: 291.8060 Evaluate side-chains 230 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 9 average time/residue: 0.2370 time to fit residues: 4.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 82 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9905 Z= 0.249 Angle : 0.572 5.952 13455 Z= 0.279 Chirality : 0.044 0.222 1479 Planarity : 0.004 0.044 1740 Dihedral : 9.283 143.156 1366 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 4.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1213 helix: -0.11 (0.25), residues: 475 sheet: -0.31 (0.34), residues: 234 loop : -2.01 (0.25), residues: 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 1.069 Fit side-chains outliers start: 44 outliers final: 29 residues processed: 235 average time/residue: 1.1201 time to fit residues: 284.5321 Evaluate side-chains 239 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 210 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 17 residues processed: 12 average time/residue: 0.2988 time to fit residues: 6.1952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 226 ASN B 131 GLN K 704 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9905 Z= 0.292 Angle : 0.581 6.107 13455 Z= 0.283 Chirality : 0.044 0.217 1479 Planarity : 0.004 0.040 1740 Dihedral : 9.197 139.197 1366 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 3.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1213 helix: -0.01 (0.24), residues: 490 sheet: -0.09 (0.35), residues: 234 loop : -2.08 (0.25), residues: 489 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 203 time to evaluate : 1.163 Fit side-chains outliers start: 36 outliers final: 29 residues processed: 229 average time/residue: 1.0821 time to fit residues: 268.1816 Evaluate side-chains 226 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.231 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 7 average time/residue: 0.1935 time to fit residues: 3.7584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 117 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 226 ASN B 6 HIS B 134 GLN K 455 GLN K 534 ASN K 704 ASN K 732 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.033 9905 Z= 0.252 Angle : 0.565 6.194 13455 Z= 0.274 Chirality : 0.043 0.201 1479 Planarity : 0.004 0.040 1740 Dihedral : 9.051 137.424 1366 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.24), residues: 1213 helix: 0.18 (0.25), residues: 490 sheet: 0.06 (0.35), residues: 234 loop : -1.97 (0.26), residues: 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 1.239 Fit side-chains outliers start: 41 outliers final: 32 residues processed: 229 average time/residue: 1.1639 time to fit residues: 287.7376 Evaluate side-chains 227 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.298 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 10 average time/residue: 0.5417 time to fit residues: 7.9549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 71 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 226 ASN A 300 ASN B 348 ASN B 416 ASN K 455 GLN K 704 ASN K 732 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 9905 Z= 0.198 Angle : 0.550 6.648 13455 Z= 0.265 Chirality : 0.042 0.191 1479 Planarity : 0.004 0.039 1740 Dihedral : 8.877 135.307 1366 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.80 % Favored : 96.12 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.24), residues: 1213 helix: 0.40 (0.25), residues: 489 sheet: 0.20 (0.36), residues: 232 loop : -1.90 (0.26), residues: 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 191 time to evaluate : 1.580 Fit side-chains outliers start: 35 outliers final: 27 residues processed: 219 average time/residue: 1.1235 time to fit residues: 265.5971 Evaluate side-chains 215 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 6 average time/residue: 0.3576 time to fit residues: 4.3035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 131 GLN K 704 ASN K 719 ASN K 732 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9905 Z= 0.246 Angle : 0.562 6.752 13455 Z= 0.271 Chirality : 0.043 0.194 1479 Planarity : 0.004 0.039 1740 Dihedral : 8.890 135.644 1366 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.36 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.24), residues: 1213 helix: 0.42 (0.25), residues: 490 sheet: 0.25 (0.35), residues: 232 loop : -1.84 (0.26), residues: 491 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 1.226 Fit side-chains outliers start: 39 outliers final: 24 residues processed: 223 average time/residue: 1.0916 time to fit residues: 262.9954 Evaluate side-chains 223 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 199 time to evaluate : 1.145 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.3589 time to fit residues: 3.3303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.0170 chunk 98 optimal weight: 0.9980 chunk 102 optimal weight: 0.0470 chunk 108 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 114 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 overall best weight: 0.1336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 226 ASN B 100 ASN B 131 GLN B 292 GLN K 704 ASN K 732 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 9905 Z= 0.131 Angle : 0.520 8.107 13455 Z= 0.248 Chirality : 0.041 0.174 1479 Planarity : 0.004 0.038 1740 Dihedral : 8.488 131.675 1366 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.89 % Favored : 97.02 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1213 helix: 0.75 (0.25), residues: 482 sheet: 0.47 (0.36), residues: 225 loop : -1.65 (0.26), residues: 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 202 time to evaluate : 1.431 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 226 average time/residue: 1.0744 time to fit residues: 262.5608 Evaluate side-chains 208 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 191 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 16 residues processed: 1 average time/residue: 0.0903 time to fit residues: 1.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 chunk 29 optimal weight: 0.0670 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 424 GLN K 455 GLN K 704 ASN K 719 ASN K 732 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 9905 Z= 0.175 Angle : 0.536 6.925 13455 Z= 0.257 Chirality : 0.042 0.177 1479 Planarity : 0.004 0.060 1740 Dihedral : 8.518 132.916 1366 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.25), residues: 1213 helix: 0.82 (0.25), residues: 482 sheet: 0.45 (0.35), residues: 232 loop : -1.56 (0.27), residues: 499 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.217 Fit side-chains outliers start: 20 outliers final: 18 residues processed: 209 average time/residue: 1.1554 time to fit residues: 261.2983 Evaluate side-chains 208 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.203 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 15 residues processed: 3 average time/residue: 0.1522 time to fit residues: 2.2788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.0070 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN B 131 GLN B 424 GLN K 534 ASN K 704 ASN K 719 ASN K 732 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.127768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110460 restraints weight = 21245.254| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.49 r_work: 0.3374 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9905 Z= 0.200 Angle : 0.548 6.696 13455 Z= 0.264 Chirality : 0.042 0.178 1479 Planarity : 0.004 0.065 1740 Dihedral : 8.567 133.653 1366 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1213 helix: 0.74 (0.25), residues: 489 sheet: 0.47 (0.35), residues: 234 loop : -1.58 (0.27), residues: 490 =============================================================================== Job complete usr+sys time: 4709.24 seconds wall clock time: 83 minutes 53.23 seconds (5033.23 seconds total)