Starting phenix.real_space_refine (version: dev) on Fri May 13 02:56:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/05_2022/6wwu_21948_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/05_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_21948/05_2022/6wwu_21948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/05_2022/6wwu_21948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/05_2022/6wwu_21948_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwu_21948/05_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 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 19, 'TRANS': 410, 'PCIS': 1} 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: {'GTP': 1, ' MG': 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: 7.54, per 1000 atoms: 0.78 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: 4.08 Conformation dependent library (CDL) restraints added in 2.0 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: 1.01 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: 2.53 Time building geometry restraints manager: 4.30 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: 2.580 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: 0.000 Extract box with map and model: 14.410 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 32.650 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.630 ------------------------------------------------------------------------------- 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 : 1.095 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 300 average time/residue: 0.9450 time to fit residues: 308.3785 Evaluate side-chains 218 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 209 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.1713 time to fit residues: 1.9036 ------------------------------------------------------------------------------- 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 206 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 9905 Z= 0.307 Angle : 0.648 7.309 13455 Z= 0.323 Chirality : 0.046 0.249 1479 Planarity : 0.006 0.081 1740 Dihedral : 9.866 153.689 1366 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 3.35 % 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: -2.44 (0.22), residues: 1213 helix: -1.02 (0.23), residues: 476 sheet: -0.92 (0.33), residues: 238 loop : -2.50 (0.25), residues: 499 *********************** 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 250 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 1.128 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 237 average time/residue: 0.9635 time to fit residues: 248.8363 Evaluate side-chains 219 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 200 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 15 residues processed: 4 average time/residue: 0.4921 time to fit residues: 3.9109 ------------------------------------------------------------------------------- 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: 3.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN B 131 GLN B 291 GLN B 334 GLN K 475 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 9905 Z= 0.288 Angle : 0.599 6.027 13455 Z= 0.296 Chirality : 0.044 0.211 1479 Planarity : 0.005 0.083 1740 Dihedral : 9.481 146.844 1366 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.70 (0.23), residues: 1213 helix: -0.39 (0.24), residues: 473 sheet: -0.45 (0.34), residues: 234 loop : -2.14 (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: 41 poor density : 226 time to evaluate : 1.171 Fit side-chains outliers start: 41 outliers final: 24 residues processed: 246 average time/residue: 1.0952 time to fit residues: 291.3721 Evaluate side-chains 225 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 201 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 14 residues processed: 10 average time/residue: 0.3480 time to fit residues: 5.9135 ------------------------------------------------------------------------------- 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: 0.2980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.0370 chunk 110 optimal weight: 0.0170 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 K 704 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3780 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= 0.187 Angle : 0.548 5.949 13455 Z= 0.266 Chirality : 0.042 0.211 1479 Planarity : 0.004 0.047 1740 Dihedral : 9.054 138.807 1366 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % 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: -1.22 (0.24), residues: 1213 helix: 0.01 (0.25), residues: 480 sheet: -0.05 (0.35), residues: 225 loop : -1.95 (0.25), residues: 508 *********************** 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 252 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 211 time to evaluate : 1.203 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 232 average time/residue: 1.0382 time to fit residues: 261.0381 Evaluate side-chains 225 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 13 residues processed: 9 average time/residue: 0.3423 time to fit residues: 5.4151 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 0.0980 chunk 99 optimal weight: 0.0170 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 256 GLN B 100 ASN B 131 GLN B 291 GLN B 424 GLN K 704 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 9905 Z= 0.189 Angle : 0.542 5.788 13455 Z= 0.262 Chirality : 0.042 0.202 1479 Planarity : 0.004 0.040 1740 Dihedral : 8.885 135.158 1366 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 3.07 % 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: -1.00 (0.24), residues: 1213 helix: 0.17 (0.25), residues: 488 sheet: 0.14 (0.36), residues: 225 loop : -1.87 (0.25), residues: 500 *********************** 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 236 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 1.051 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 226 average time/residue: 1.0830 time to fit residues: 264.5806 Evaluate side-chains 214 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.3632 time to fit residues: 3.8139 ------------------------------------------------------------------------------- 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: 1.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 B 348 ASN B 424 GLN K 455 GLN K 704 ASN K 732 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 9905 Z= 0.411 Angle : 0.630 7.103 13455 Z= 0.307 Chirality : 0.046 0.217 1479 Planarity : 0.005 0.041 1740 Dihedral : 9.240 139.814 1366 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.38 % Favored : 95.54 % Rotamer Outliers : 3.74 % 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: 0.08 (0.25), residues: 481 sheet: 0.02 (0.35), residues: 236 loop : -1.80 (0.26), residues: 496 *********************** 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 239 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 1.073 Fit side-chains outliers start: 38 outliers final: 26 residues processed: 223 average time/residue: 1.1248 time to fit residues: 270.4369 Evaluate side-chains 222 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.3378 time to fit residues: 4.9129 ------------------------------------------------------------------------------- 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: 0.8980 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 98 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 71 optimal weight: 0.0570 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.3980 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 216 ASN A 226 ASN A 300 ASN K 534 ASN K 704 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9905 Z= 0.176 Angle : 0.546 6.807 13455 Z= 0.263 Chirality : 0.042 0.189 1479 Planarity : 0.004 0.038 1740 Dihedral : 8.875 135.131 1366 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer Outliers : 3.07 % 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: 0.34 (0.25), residues: 484 sheet: 0.24 (0.35), residues: 234 loop : -1.70 (0.26), residues: 495 *********************** 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 225 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.106 Fit side-chains outliers start: 31 outliers final: 24 residues processed: 214 average time/residue: 1.1228 time to fit residues: 260.7514 Evaluate side-chains 213 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.118 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.3161 time to fit residues: 4.3762 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN K 455 GLN K 534 ASN K 704 ASN K 732 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 9905 Z= 0.358 Angle : 0.612 6.443 13455 Z= 0.299 Chirality : 0.045 0.205 1479 Planarity : 0.005 0.040 1740 Dihedral : 9.112 138.746 1366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.70 % Rotamer Outliers : 2.97 % 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: -0.87 (0.24), residues: 1213 helix: 0.24 (0.25), residues: 485 sheet: 0.08 (0.35), residues: 236 loop : -1.72 (0.26), residues: 492 *********************** 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 226 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 0.973 Fit side-chains outliers start: 30 outliers final: 21 residues processed: 218 average time/residue: 1.0638 time to fit residues: 251.2090 Evaluate side-chains 212 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.0914 time to fit residues: 2.0447 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 0.5980 chunk 47 optimal weight: 0.0870 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 534 ASN K 704 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9905 Z= 0.227 Angle : 0.567 6.413 13455 Z= 0.275 Chirality : 0.043 0.192 1479 Planarity : 0.004 0.061 1740 Dihedral : 8.904 136.460 1366 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.39 % Favored : 96.53 % Rotamer Outliers : 2.78 % 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: -0.73 (0.24), residues: 1213 helix: 0.33 (0.25), residues: 489 sheet: 0.24 (0.35), residues: 234 loop : -1.66 (0.26), residues: 490 *********************** 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 223 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.226 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 216 average time/residue: 1.0766 time to fit residues: 251.8367 Evaluate side-chains 214 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 193 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.7229 time to fit residues: 3.9671 ------------------------------------------------------------------------------- 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: 0.8980 chunk 79 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 110 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 102 optimal weight: 0.2980 chunk 29 optimal weight: 0.0270 overall best weight: 0.3038 ------------------------------------------------------------------------------- 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 534 ASN K 704 ASN K 732 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9905 Z= 0.171 Angle : 0.541 6.465 13455 Z= 0.261 Chirality : 0.041 0.186 1479 Planarity : 0.004 0.064 1740 Dihedral : 8.717 133.659 1366 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.47 % Favored : 96.45 % Rotamer Outliers : 2.11 % 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: -0.42 (0.25), residues: 1213 helix: 0.66 (0.25), residues: 479 sheet: 0.33 (0.35), residues: 232 loop : -1.49 (0.27), residues: 502 ********************** 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 216 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 1.093 Fit side-chains outliers start: 21 outliers final: 19 residues processed: 214 average time/residue: 1.0861 time to fit residues: 250.9971 Evaluate side-chains 214 residues out of total 1042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 195 time to evaluate : 1.053 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0881 time to fit residues: 1.6407 ------------------------------------------------------------------------------- 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: 0.7980 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 84 optimal weight: 0.4980 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.5238 ------------------------------------------------------------------------------- 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 416 ASN K 534 ASN K 704 ASN K 732 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110131 restraints weight = 18897.759| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.30 r_work: 0.3481 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3446 rms_B_bonded: 2.12 restraints_weight: 0.1250 r_work: 0.3427 rms_B_bonded: 2.26 restraints_weight: 0.0625 r_work: 0.3405 rms_B_bonded: 2.47 restraints_weight: 0.0312 r_work: 0.3381 rms_B_bonded: 2.74 restraints_weight: 0.0156 r_work: 0.3354 rms_B_bonded: 3.08 restraints_weight: 0.0078 r_work: 0.3322 rms_B_bonded: 3.50 restraints_weight: 0.0039 r_work: 0.3287 rms_B_bonded: 4.00 restraints_weight: 0.0020 r_work: 0.3246 rms_B_bonded: 4.62 restraints_weight: 0.0010 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9905 Z= 0.227 Angle : 0.564 6.492 13455 Z= 0.274 Chirality : 0.043 0.190 1479 Planarity : 0.005 0.097 1740 Dihedral : 8.806 135.170 1366 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.36 % Rotamer Outliers : 2.49 % 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: -0.47 (0.25), residues: 1213 helix: 0.59 (0.25), residues: 492 sheet: 0.39 (0.35), residues: 232 loop : -1.58 (0.27), residues: 489 =============================================================================== Job complete usr+sys time: 4339.43 seconds wall clock time: 77 minutes 23.46 seconds (4643.46 seconds total)