Starting phenix.real_space_refine on Wed Feb 14 20:23:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rag_4774/02_2024/6rag_4774_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 25 5.16 5 C 6568 2.51 5 N 1797 2.21 5 O 1791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 11": "OD1" <-> "OD2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10188 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4690 Classifications: {'peptide': 586} Link IDs: {'PTRANS': 24, 'TRANS': 561} Chain: "B" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4541 Classifications: {'peptide': 575} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 556} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.44, per 1000 atoms: 0.53 Number of scatterers: 10188 At special positions: 0 Unit cell: (102.315, 92.622, 155.088, 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 25 16.00 P 5 15.00 Mg 2 11.99 O 1791 8.00 N 1797 7.00 C 6568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 3.87 Conformation dependent library (CDL) restraints added in 1.8 seconds 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 7 sheets defined 59.2% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 12 through 44 removed outlier: 4.261A pdb=" N ILE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) Proline residue: A 24 - end of helix removed outlier: 5.867A pdb=" N LEU A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLN A 28 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 65 through 75 removed outlier: 5.012A pdb=" N LEU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 74 " --> pdb=" O PHE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 118 Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.828A pdb=" N ASP A 126 " --> pdb=" O GLY A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 172 removed outlier: 3.576A pdb=" N THR A 138 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL A 141 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.461A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 221 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 232 through 257 removed outlier: 3.742A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 290 through 312 removed outlier: 3.657A pdb=" N VAL A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 5.601A pdb=" N ASP A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 331 removed outlier: 3.645A pdb=" N GLY A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 399 through 406 Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 476 through 479 No H-bonds generated for 'chain 'A' and resid 476 through 479' Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.774A pdb=" N VAL A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'B' and resid 6 through 53 Proline residue: B 15 - end of helix removed outlier: 3.773A pdb=" N ARG B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR B 20 " --> pdb=" O TYR B 16 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 58 through 104 removed outlier: 3.701A pdb=" N SER B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 4.140A pdb=" N LYS B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.534A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 206 removed outlier: 3.658A pdb=" N TYR B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.563A pdb=" N PHE B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 217 through 242 removed outlier: 3.763A pdb=" N ALA B 222 " --> pdb=" O ARG B 218 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 270 removed outlier: 3.835A pdb=" N ALA B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.521A pdb=" N LEU B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 317 removed outlier: 3.570A pdb=" N LEU B 293 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TRP B 297 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 304 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 308 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 316 " --> pdb=" O PHE B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.804A pdb=" N ALA B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLY B 435 " --> pdb=" O ASN B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 451 Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 477 through 490 Processing helix chain 'B' and resid 507 through 520 removed outlier: 3.972A pdb=" N VAL B 520 " --> pdb=" O GLY B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 removed outlier: 4.348A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 561 removed outlier: 3.693A pdb=" N GLN B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 577 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 381 through 383 removed outlier: 3.568A pdb=" N VAL A 353 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 572 through 577 removed outlier: 6.867A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER A 549 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU A 391 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE A 551 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 394 through 397 removed outlier: 4.964A pdb=" N LEU B 357 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 550 through 554 removed outlier: 6.818A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TRP B 541 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU B 545 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR B 526 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ILE B 369 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU B 528 " --> pdb=" O ILE B 369 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.660A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.529A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 101 through 103 removed outlier: 3.930A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1635 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: 3.09 Time building geometry restraints manager: 4.17 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: 1615 1.31 - 1.44: 2800 1.44 - 1.56: 5924 1.56 - 1.69: 16 1.69 - 1.81: 45 Bond restraints: 10400 Sorted by residual: bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.79e+01 bond pdb=" C5 ATP B 602 " pdb=" C6 ATP B 602 " ideal model delta sigma weight residual 1.409 1.474 -0.065 1.00e-02 1.00e+04 4.21e+01 bond pdb=" N PRO A 515 " pdb=" CD PRO A 515 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.55e+01 bond pdb=" CA PHE A 296 " pdb=" C PHE A 296 " ideal model delta sigma weight residual 1.522 1.593 -0.071 1.39e-02 5.18e+03 2.57e+01 bond pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 1.374 1.326 0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 10395 not shown) Histogram of bond angle deviations from ideal: 98.04 - 105.70: 252 105.70 - 113.35: 5631 113.35 - 121.01: 5526 121.01 - 128.67: 2620 128.67 - 136.33: 82 Bond angle restraints: 14111 Sorted by residual: angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 119.93 19.94 1.00e+00 1.00e+00 3.98e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 118.46 18.37 1.00e+00 1.00e+00 3.37e+02 angle pdb=" N VAL B 298 " pdb=" CA VAL B 298 " pdb=" C VAL B 298 " ideal model delta sigma weight residual 110.53 98.04 12.49 9.40e-01 1.13e+00 1.77e+02 angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 112.64 123.80 -11.16 1.21e+00 6.83e-01 8.51e+01 angle pdb=" N LEU B 536 " pdb=" CA LEU B 536 " pdb=" C LEU B 536 " ideal model delta sigma weight residual 112.97 103.27 9.70 1.06e+00 8.90e-01 8.37e+01 ... (remaining 14106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 5955 29.84 - 59.67: 212 59.67 - 89.51: 22 89.51 - 119.34: 1 119.34 - 149.17: 2 Dihedral angle restraints: 6192 sinusoidal: 2527 harmonic: 3665 Sorted by residual: dihedral pdb=" O1B ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PB ADP A 702 " pdb=" PA ADP A 702 " ideal model delta sinusoidal sigma weight residual 300.00 150.82 149.17 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O2A ADP A 702 " pdb=" O3A ADP A 702 " pdb=" PA ADP A 702 " pdb=" PB ADP A 702 " ideal model delta sinusoidal sigma weight residual -60.00 62.82 -122.82 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" CA TRP B 290 " pdb=" C TRP B 290 " pdb=" N PRO B 291 " pdb=" CA PRO B 291 " ideal model delta harmonic sigma weight residual -180.00 -150.78 -29.22 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1335 0.096 - 0.191: 229 0.191 - 0.287: 29 0.287 - 0.383: 9 0.383 - 0.478: 7 Chirality restraints: 1609 Sorted by residual: chirality pdb=" CA ASP B 500 " pdb=" N ASP B 500 " pdb=" C ASP B 500 " pdb=" CB ASP B 500 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA VAL C 102 " pdb=" N VAL C 102 " pdb=" C VAL C 102 " pdb=" CB VAL C 102 " both_signs ideal model delta sigma weight residual False 2.44 2.90 -0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 1606 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 138 " 0.023 2.00e-02 2.50e+03 4.74e-02 2.25e+01 pdb=" C THR A 138 " -0.082 2.00e-02 2.50e+03 pdb=" O THR A 138 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 139 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 23 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 24 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 24 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 24 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 243 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.19e+00 pdb=" N PRO B 244 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " -0.040 5.00e-02 4.00e+02 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 34 2.51 - 3.11: 7109 3.11 - 3.70: 16004 3.70 - 4.30: 21246 4.30 - 4.90: 34452 Nonbonded interactions: 78845 Sorted by model distance: nonbonded pdb="MG MG B 601 " pdb=" O1B ATP B 602 " model vdw 1.911 2.170 nonbonded pdb="MG MG B 601 " pdb=" O1G ATP B 602 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN B 419 " pdb="MG MG B 601 " model vdw 2.024 2.170 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 601 " model vdw 2.050 2.170 nonbonded pdb=" O THR A 400 " pdb=" OG SER A 404 " model vdw 2.252 2.440 ... (remaining 78840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 3.890 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.860 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.010 0.103 10400 Z= 0.621 Angle : 1.420 19.938 14111 Z= 0.926 Chirality : 0.079 0.478 1609 Planarity : 0.008 0.078 1785 Dihedral : 15.357 149.175 3840 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.67 % Allowed : 12.20 % Favored : 87.13 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 0.00 % 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: -3.67 (0.18), residues: 1276 helix: -2.48 (0.14), residues: 768 sheet: -0.57 (0.43), residues: 124 loop : -2.52 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 193 HIS 0.012 0.002 HIS B 100 PHE 0.025 0.003 PHE A 147 TYR 0.029 0.003 TYR A 588 ARG 0.011 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 273 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 PHE cc_start: 0.7289 (m-10) cc_final: 0.7011 (m-80) REVERT: A 118 MET cc_start: 0.9224 (mmt) cc_final: 0.9007 (tpp) REVERT: A 166 LEU cc_start: 0.8440 (tp) cc_final: 0.7972 (tt) REVERT: A 205 MET cc_start: 0.8817 (tmm) cc_final: 0.8548 (tmm) REVERT: A 218 GLU cc_start: 0.8421 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 375 VAL cc_start: 0.0141 (OUTLIER) cc_final: -0.0356 (t) REVERT: A 430 GLU cc_start: 0.8154 (pt0) cc_final: 0.7393 (mt-10) REVERT: A 508 VAL cc_start: 0.8884 (p) cc_final: 0.8679 (m) REVERT: A 560 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8472 (tpp80) REVERT: B 25 LEU cc_start: 0.8800 (tp) cc_final: 0.8360 (tt) REVERT: B 32 LEU cc_start: 0.8447 (mt) cc_final: 0.8210 (mp) REVERT: B 154 MET cc_start: 0.8952 (ttt) cc_final: 0.8295 (ttt) REVERT: B 191 GLN cc_start: 0.8146 (pp30) cc_final: 0.7895 (tm-30) REVERT: B 228 ASN cc_start: 0.9239 (t0) cc_final: 0.8898 (t0) REVERT: B 253 MET cc_start: 0.8825 (mmt) cc_final: 0.8625 (mmp) REVERT: B 347 LYS cc_start: 0.7606 (tptt) cc_final: 0.7003 (tppt) REVERT: B 412 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8478 (mtmm) REVERT: B 436 LEU cc_start: 0.9108 (tp) cc_final: 0.8888 (tp) REVERT: B 521 LEU cc_start: 0.8826 (tp) cc_final: 0.8469 (mp) REVERT: B 558 SER cc_start: 0.9095 (m) cc_final: 0.8819 (t) REVERT: B 559 LEU cc_start: 0.9062 (mt) cc_final: 0.8849 (mt) REVERT: B 569 MET cc_start: 0.6915 (ttm) cc_final: 0.6457 (ttm) REVERT: C 37 PHE cc_start: 0.8313 (m-80) cc_final: 0.8092 (m-80) REVERT: C 53 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8765 (ttmt) REVERT: C 93 VAL cc_start: 0.8760 (m) cc_final: 0.8357 (p) REVERT: C 98 THR cc_start: 0.8955 (m) cc_final: 0.8630 (t) REVERT: C 109 VAL cc_start: 0.8536 (t) cc_final: 0.8227 (t) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.2693 time to fit residues: 101.0313 Evaluate side-chains 186 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 181 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 453 ASN ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 111 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 479 GLN B 531 HIS B 556 HIS C 3 GLN C 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10400 Z= 0.246 Angle : 0.683 6.491 14111 Z= 0.352 Chirality : 0.043 0.170 1609 Planarity : 0.006 0.061 1785 Dihedral : 7.100 115.090 1483 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.19 % Allowed : 6.67 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % 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: -1.48 (0.21), residues: 1276 helix: -0.51 (0.17), residues: 758 sheet: -0.57 (0.40), residues: 138 loop : -1.85 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 193 HIS 0.006 0.001 HIS B 111 PHE 0.022 0.002 PHE A 160 TYR 0.015 0.002 TYR A 588 ARG 0.007 0.001 ARG A 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 LEU cc_start: 0.8358 (mm) cc_final: 0.7801 (tp) REVERT: A 455 ARG cc_start: 0.8229 (ptt180) cc_final: 0.7735 (ptt-90) REVERT: A 502 LYS cc_start: 0.8799 (mtmt) cc_final: 0.8545 (mtmt) REVERT: B 25 LEU cc_start: 0.8769 (tp) cc_final: 0.8487 (tt) REVERT: B 32 LEU cc_start: 0.8465 (mt) cc_final: 0.8194 (mp) REVERT: B 125 ASP cc_start: 0.7019 (m-30) cc_final: 0.6770 (m-30) REVERT: B 154 MET cc_start: 0.8977 (ttt) cc_final: 0.8172 (ttt) REVERT: B 186 ARG cc_start: 0.8282 (mmt-90) cc_final: 0.8064 (mmt-90) REVERT: B 228 ASN cc_start: 0.9209 (t0) cc_final: 0.8894 (t0) REVERT: B 252 LEU cc_start: 0.9305 (mm) cc_final: 0.9010 (mm) REVERT: B 253 MET cc_start: 0.8895 (mmt) cc_final: 0.8525 (mmp) REVERT: B 347 LYS cc_start: 0.7497 (tptt) cc_final: 0.6803 (tppt) REVERT: B 365 MET cc_start: 0.8236 (tmm) cc_final: 0.7987 (tmm) REVERT: B 367 LEU cc_start: 0.9628 (tp) cc_final: 0.9378 (tt) REVERT: B 430 GLU cc_start: 0.7764 (tp30) cc_final: 0.7550 (tp30) REVERT: B 558 SER cc_start: 0.9295 (m) cc_final: 0.9062 (t) REVERT: B 569 MET cc_start: 0.7128 (ttm) cc_final: 0.6548 (ttm) REVERT: C 3 GLN cc_start: 0.5434 (pt0) cc_final: 0.3946 (pt0) REVERT: C 53 LYS cc_start: 0.8995 (ttpp) cc_final: 0.8786 (tppt) REVERT: C 57 ASN cc_start: 0.7842 (m-40) cc_final: 0.6810 (t0) REVERT: C 65 LYS cc_start: 0.8876 (ptmt) cc_final: 0.8381 (mttt) REVERT: C 93 VAL cc_start: 0.8726 (m) cc_final: 0.8303 (p) REVERT: C 94 TYR cc_start: 0.5847 (m-80) cc_final: 0.5615 (m-10) REVERT: C 104 LEU cc_start: 0.7326 (tp) cc_final: 0.6735 (tt) REVERT: C 109 VAL cc_start: 0.8304 (t) cc_final: 0.8085 (t) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.2745 time to fit residues: 86.2326 Evaluate side-chains 167 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 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 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS B 538 HIS C 39 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10400 Z= 0.192 Angle : 0.606 6.709 14111 Z= 0.308 Chirality : 0.041 0.157 1609 Planarity : 0.004 0.057 1785 Dihedral : 6.433 104.423 1483 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.23), residues: 1276 helix: 0.42 (0.18), residues: 764 sheet: -0.40 (0.41), residues: 126 loop : -1.63 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 36 HIS 0.005 0.001 HIS B 100 PHE 0.011 0.001 PHE C 68 TYR 0.012 0.001 TYR C 113 ARG 0.003 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9416 (p) cc_final: 0.9165 (t) REVERT: A 376 LEU cc_start: 0.6201 (mt) cc_final: 0.5864 (mt) REVERT: A 405 LEU cc_start: 0.8192 (tp) cc_final: 0.7882 (tp) REVERT: A 445 LEU cc_start: 0.8264 (mm) cc_final: 0.7683 (tp) REVERT: B 25 LEU cc_start: 0.8705 (tp) cc_final: 0.8449 (tt) REVERT: B 125 ASP cc_start: 0.7015 (m-30) cc_final: 0.6770 (m-30) REVERT: B 154 MET cc_start: 0.8948 (ttt) cc_final: 0.8041 (ttt) REVERT: B 191 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 199 THR cc_start: 0.9002 (m) cc_final: 0.8661 (m) REVERT: B 347 LYS cc_start: 0.7523 (tptt) cc_final: 0.6856 (tppt) REVERT: B 365 MET cc_start: 0.8109 (tmm) cc_final: 0.7741 (tmm) REVERT: B 367 LEU cc_start: 0.9627 (tp) cc_final: 0.9372 (tt) REVERT: B 412 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8278 (mtmm) REVERT: B 423 LEU cc_start: 0.8930 (mt) cc_final: 0.8593 (pp) REVERT: B 436 LEU cc_start: 0.8812 (tp) cc_final: 0.8308 (tt) REVERT: B 521 LEU cc_start: 0.8518 (mt) cc_final: 0.8179 (mp) REVERT: B 558 SER cc_start: 0.9337 (m) cc_final: 0.9118 (t) REVERT: B 569 MET cc_start: 0.7032 (ttm) cc_final: 0.6417 (ttm) REVERT: C 53 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8735 (tppt) REVERT: C 57 ASN cc_start: 0.7815 (m-40) cc_final: 0.6839 (t0) REVERT: C 65 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8485 (mttt) REVERT: C 93 VAL cc_start: 0.8924 (m) cc_final: 0.8596 (p) REVERT: C 104 LEU cc_start: 0.6989 (tp) cc_final: 0.6512 (tt) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.2355 time to fit residues: 74.8348 Evaluate side-chains 162 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 3 GLN C 39 GLN C 80 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10400 Z= 0.233 Angle : 0.635 7.530 14111 Z= 0.320 Chirality : 0.042 0.171 1609 Planarity : 0.004 0.051 1785 Dihedral : 6.157 104.805 1483 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.10 % Allowed : 4.10 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.23), residues: 1276 helix: 0.71 (0.19), residues: 767 sheet: -0.44 (0.40), residues: 139 loop : -1.54 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 36 HIS 0.005 0.001 HIS B 100 PHE 0.019 0.001 PHE A 160 TYR 0.015 0.001 TYR A 299 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9566 (p) cc_final: 0.9259 (t) REVERT: A 256 TRP cc_start: 0.7462 (m100) cc_final: 0.7180 (m100) REVERT: A 299 TYR cc_start: 0.8644 (m-80) cc_final: 0.8345 (m-80) REVERT: A 376 LEU cc_start: 0.6132 (mt) cc_final: 0.5924 (mt) REVERT: A 405 LEU cc_start: 0.8273 (tp) cc_final: 0.8018 (tp) REVERT: A 444 PHE cc_start: 0.7169 (t80) cc_final: 0.6554 (t80) REVERT: A 445 LEU cc_start: 0.8401 (mm) cc_final: 0.8063 (tp) REVERT: A 501 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7389 (mt-10) REVERT: B 25 LEU cc_start: 0.8808 (tp) cc_final: 0.8512 (tt) REVERT: B 125 ASP cc_start: 0.7130 (m-30) cc_final: 0.6859 (m-30) REVERT: B 154 MET cc_start: 0.8976 (ttt) cc_final: 0.8458 (ttt) REVERT: B 365 MET cc_start: 0.8210 (tmm) cc_final: 0.7945 (tmm) REVERT: B 367 LEU cc_start: 0.9640 (tp) cc_final: 0.9407 (tt) REVERT: B 569 MET cc_start: 0.7163 (ttm) cc_final: 0.6474 (ttm) REVERT: B 573 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8308 (tp-100) REVERT: C 53 LYS cc_start: 0.9094 (ttpp) cc_final: 0.8738 (tppt) REVERT: C 57 ASN cc_start: 0.7746 (m-40) cc_final: 0.6930 (t0) REVERT: C 65 LYS cc_start: 0.8912 (ptmt) cc_final: 0.8437 (mttt) REVERT: C 93 VAL cc_start: 0.8918 (m) cc_final: 0.8532 (p) REVERT: C 94 TYR cc_start: 0.6106 (m-80) cc_final: 0.5746 (m-80) REVERT: C 104 LEU cc_start: 0.6981 (tp) cc_final: 0.6509 (tt) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2208 time to fit residues: 67.1091 Evaluate side-chains 156 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 538 HIS C 3 GLN C 39 GLN C 57 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10400 Z= 0.167 Angle : 0.594 6.464 14111 Z= 0.294 Chirality : 0.041 0.157 1609 Planarity : 0.004 0.052 1785 Dihedral : 5.758 97.886 1483 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.19 % Allowed : 2.48 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.23), residues: 1276 helix: 0.98 (0.19), residues: 769 sheet: -0.25 (0.40), residues: 146 loop : -1.28 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 36 HIS 0.005 0.001 HIS A 476 PHE 0.016 0.001 PHE A 478 TYR 0.038 0.001 TYR B 187 ARG 0.003 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9536 (p) cc_final: 0.9260 (t) REVERT: A 99 GLN cc_start: 0.8836 (mm110) cc_final: 0.8635 (mt0) REVERT: A 112 ASP cc_start: 0.8848 (t0) cc_final: 0.8305 (t70) REVERT: A 169 MET cc_start: 0.8398 (mmm) cc_final: 0.8185 (mmp) REVERT: A 256 TRP cc_start: 0.7398 (m100) cc_final: 0.6809 (m100) REVERT: A 299 TYR cc_start: 0.8364 (m-80) cc_final: 0.8125 (m-80) REVERT: A 376 LEU cc_start: 0.6441 (mt) cc_final: 0.6241 (mt) REVERT: A 405 LEU cc_start: 0.8237 (tp) cc_final: 0.7986 (tp) REVERT: A 444 PHE cc_start: 0.7042 (t80) cc_final: 0.6562 (t80) REVERT: A 445 LEU cc_start: 0.8426 (mm) cc_final: 0.8075 (tp) REVERT: B 25 LEU cc_start: 0.8734 (tp) cc_final: 0.8450 (tt) REVERT: B 125 ASP cc_start: 0.7109 (m-30) cc_final: 0.6857 (m-30) REVERT: B 154 MET cc_start: 0.8941 (ttt) cc_final: 0.8057 (ttt) REVERT: B 199 THR cc_start: 0.8887 (m) cc_final: 0.8606 (m) REVERT: B 319 LYS cc_start: 0.8283 (tptt) cc_final: 0.8068 (tmtt) REVERT: B 365 MET cc_start: 0.8165 (tmm) cc_final: 0.7699 (tmm) REVERT: B 367 LEU cc_start: 0.9642 (tp) cc_final: 0.9415 (tt) REVERT: B 556 HIS cc_start: 0.8202 (p-80) cc_final: 0.7917 (t70) REVERT: B 559 LEU cc_start: 0.9275 (mt) cc_final: 0.9072 (mt) REVERT: B 569 MET cc_start: 0.7145 (ttm) cc_final: 0.6410 (ttm) REVERT: C 3 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: C 53 LYS cc_start: 0.8992 (ttpp) cc_final: 0.8742 (tppt) REVERT: C 57 ASN cc_start: 0.7724 (m110) cc_final: 0.7059 (t0) REVERT: C 65 LYS cc_start: 0.8880 (ptmt) cc_final: 0.8421 (mttt) REVERT: C 93 VAL cc_start: 0.8854 (m) cc_final: 0.8427 (p) REVERT: C 94 TYR cc_start: 0.6082 (m-80) cc_final: 0.5569 (m-80) REVERT: C 104 LEU cc_start: 0.7039 (tp) cc_final: 0.6675 (tt) outliers start: 2 outliers final: 0 residues processed: 226 average time/residue: 0.2237 time to fit residues: 71.1722 Evaluate side-chains 162 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0030 chunk 110 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 102 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10400 Z= 0.154 Angle : 0.589 6.841 14111 Z= 0.292 Chirality : 0.041 0.180 1609 Planarity : 0.004 0.053 1785 Dihedral : 5.221 80.180 1483 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.23), residues: 1276 helix: 1.27 (0.19), residues: 759 sheet: -0.13 (0.42), residues: 136 loop : -1.15 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 36 HIS 0.002 0.001 HIS B 100 PHE 0.014 0.001 PHE B 281 TYR 0.024 0.001 TYR B 187 ARG 0.006 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9559 (p) cc_final: 0.9347 (t) REVERT: A 112 ASP cc_start: 0.8835 (t0) cc_final: 0.8205 (t70) REVERT: A 405 LEU cc_start: 0.8329 (tp) cc_final: 0.8077 (tp) REVERT: A 444 PHE cc_start: 0.7060 (t80) cc_final: 0.6451 (t80) REVERT: A 445 LEU cc_start: 0.8404 (mm) cc_final: 0.8087 (tp) REVERT: A 575 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5348 (mp0) REVERT: B 25 LEU cc_start: 0.8685 (tp) cc_final: 0.8456 (tt) REVERT: B 79 MET cc_start: 0.8961 (tmm) cc_final: 0.8718 (tmm) REVERT: B 154 MET cc_start: 0.8937 (ttt) cc_final: 0.7923 (ttt) REVERT: B 199 THR cc_start: 0.8890 (m) cc_final: 0.8588 (m) REVERT: B 319 LYS cc_start: 0.8410 (tptt) cc_final: 0.8106 (tmtt) REVERT: B 365 MET cc_start: 0.8112 (tmm) cc_final: 0.7721 (tmm) REVERT: B 556 HIS cc_start: 0.8147 (p-80) cc_final: 0.7807 (t70) REVERT: B 559 LEU cc_start: 0.9250 (mt) cc_final: 0.9025 (mt) REVERT: B 569 MET cc_start: 0.6838 (ttm) cc_final: 0.6118 (ttm) REVERT: C 53 LYS cc_start: 0.9013 (ttpp) cc_final: 0.8762 (tppt) REVERT: C 57 ASN cc_start: 0.7731 (m110) cc_final: 0.6984 (t0) REVERT: C 65 LYS cc_start: 0.8868 (ptmt) cc_final: 0.8420 (mttt) REVERT: C 93 VAL cc_start: 0.8909 (m) cc_final: 0.8488 (p) REVERT: C 94 TYR cc_start: 0.6151 (m-80) cc_final: 0.5576 (m-80) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.2085 time to fit residues: 67.1617 Evaluate side-chains 163 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 70 optimal weight: 0.6980 chunk 89 optimal weight: 0.0170 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 3 GLN C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10400 Z= 0.161 Angle : 0.615 10.234 14111 Z= 0.298 Chirality : 0.041 0.226 1609 Planarity : 0.004 0.051 1785 Dihedral : 4.928 68.177 1483 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.10 % Allowed : 1.62 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.24), residues: 1276 helix: 1.36 (0.19), residues: 769 sheet: -0.04 (0.41), residues: 145 loop : -1.18 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP C 36 HIS 0.002 0.001 HIS B 100 PHE 0.018 0.001 PHE B 163 TYR 0.022 0.001 TYR B 187 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 THR cc_start: 0.9570 (p) cc_final: 0.9332 (t) REVERT: A 112 ASP cc_start: 0.8768 (t0) cc_final: 0.8182 (t70) REVERT: A 444 PHE cc_start: 0.7016 (t80) cc_final: 0.6582 (t80) REVERT: A 445 LEU cc_start: 0.8413 (mm) cc_final: 0.8034 (tt) REVERT: B 25 LEU cc_start: 0.8742 (tp) cc_final: 0.8481 (tt) REVERT: B 79 MET cc_start: 0.8991 (tmm) cc_final: 0.8716 (tmm) REVERT: B 125 ASP cc_start: 0.6979 (m-30) cc_final: 0.6734 (m-30) REVERT: B 154 MET cc_start: 0.8851 (ttt) cc_final: 0.8396 (ttp) REVERT: B 184 ASP cc_start: 0.8804 (t70) cc_final: 0.8556 (t0) REVERT: B 199 THR cc_start: 0.8871 (m) cc_final: 0.8547 (m) REVERT: B 319 LYS cc_start: 0.8442 (tptt) cc_final: 0.8136 (tmtt) REVERT: B 347 LYS cc_start: 0.7404 (tptt) cc_final: 0.6782 (tppt) REVERT: B 365 MET cc_start: 0.8188 (tmm) cc_final: 0.7824 (tmm) REVERT: B 556 HIS cc_start: 0.8097 (p-80) cc_final: 0.7827 (t70) REVERT: B 559 LEU cc_start: 0.9268 (mt) cc_final: 0.9036 (mt) REVERT: B 569 MET cc_start: 0.6782 (ttm) cc_final: 0.6019 (ttm) REVERT: C 53 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8740 (tppt) REVERT: C 57 ASN cc_start: 0.7608 (m110) cc_final: 0.7130 (t0) REVERT: C 65 LYS cc_start: 0.8951 (ptmt) cc_final: 0.8624 (mttt) REVERT: C 93 VAL cc_start: 0.8898 (m) cc_final: 0.8430 (p) REVERT: C 94 TYR cc_start: 0.6098 (m-80) cc_final: 0.5581 (m-80) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2090 time to fit residues: 62.1071 Evaluate side-chains 158 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.0270 chunk 73 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 538 HIS C 3 GLN C 80 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10400 Z= 0.165 Angle : 0.607 8.412 14111 Z= 0.298 Chirality : 0.041 0.179 1609 Planarity : 0.004 0.051 1785 Dihedral : 4.727 60.973 1483 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.10 % Allowed : 0.57 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.24), residues: 1276 helix: 1.42 (0.19), residues: 769 sheet: -0.07 (0.41), residues: 145 loop : -1.11 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 36 HIS 0.003 0.001 HIS B 101 PHE 0.017 0.001 PHE B 281 TYR 0.034 0.001 TYR A 299 ARG 0.004 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8816 (t0) cc_final: 0.8208 (t70) REVERT: A 169 MET cc_start: 0.8342 (mmp) cc_final: 0.7646 (mmm) REVERT: A 444 PHE cc_start: 0.7035 (t80) cc_final: 0.6531 (t80) REVERT: A 445 LEU cc_start: 0.8446 (mm) cc_final: 0.8064 (tp) REVERT: B 25 LEU cc_start: 0.8765 (tp) cc_final: 0.8491 (tt) REVERT: B 79 MET cc_start: 0.8984 (tmm) cc_final: 0.8613 (tmm) REVERT: B 125 ASP cc_start: 0.7088 (m-30) cc_final: 0.6874 (m-30) REVERT: B 154 MET cc_start: 0.8892 (ttt) cc_final: 0.8104 (ttt) REVERT: B 184 ASP cc_start: 0.8773 (t70) cc_final: 0.8539 (t0) REVERT: B 199 THR cc_start: 0.8907 (m) cc_final: 0.8617 (m) REVERT: B 319 LYS cc_start: 0.8468 (tptt) cc_final: 0.8176 (tmtt) REVERT: B 347 LYS cc_start: 0.7416 (tptt) cc_final: 0.6786 (tppt) REVERT: B 365 MET cc_start: 0.8172 (tmm) cc_final: 0.7789 (tmm) REVERT: B 436 LEU cc_start: 0.8879 (tp) cc_final: 0.8673 (tp) REVERT: B 556 HIS cc_start: 0.8124 (p-80) cc_final: 0.7823 (t70) REVERT: B 559 LEU cc_start: 0.9282 (mt) cc_final: 0.9046 (mt) REVERT: B 569 MET cc_start: 0.6800 (ttm) cc_final: 0.6044 (ttm) REVERT: C 53 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8671 (tppt) REVERT: C 57 ASN cc_start: 0.7504 (m110) cc_final: 0.7068 (t0) REVERT: C 65 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8442 (mttt) REVERT: C 93 VAL cc_start: 0.8870 (m) cc_final: 0.8512 (t) REVERT: C 94 TYR cc_start: 0.6109 (m-80) cc_final: 0.5585 (m-80) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.2082 time to fit residues: 61.5823 Evaluate side-chains 161 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.0050 chunk 117 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 chunk 103 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 3 GLN C 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10400 Z= 0.155 Angle : 0.610 9.774 14111 Z= 0.296 Chirality : 0.041 0.195 1609 Planarity : 0.004 0.052 1785 Dihedral : 4.530 53.370 1483 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.10 % Allowed : 0.38 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.99 (0.24), residues: 1276 helix: 1.63 (0.19), residues: 767 sheet: -0.07 (0.41), residues: 146 loop : -1.11 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP C 36 HIS 0.002 0.001 HIS B 111 PHE 0.021 0.001 PHE B 163 TYR 0.023 0.001 TYR A 299 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8942 (pp20) cc_final: 0.8680 (pp20) REVERT: A 112 ASP cc_start: 0.8814 (t0) cc_final: 0.8223 (t70) REVERT: A 205 MET cc_start: 0.8873 (tmm) cc_final: 0.8539 (tmm) REVERT: A 444 PHE cc_start: 0.6968 (t80) cc_final: 0.6663 (t80) REVERT: A 445 LEU cc_start: 0.8436 (mm) cc_final: 0.8009 (tt) REVERT: B 25 LEU cc_start: 0.8740 (tp) cc_final: 0.8462 (tt) REVERT: B 79 MET cc_start: 0.8961 (tmm) cc_final: 0.8593 (tmm) REVERT: B 125 ASP cc_start: 0.6951 (m-30) cc_final: 0.6737 (m-30) REVERT: B 154 MET cc_start: 0.8832 (ttt) cc_final: 0.8348 (ttp) REVERT: B 184 ASP cc_start: 0.8761 (t70) cc_final: 0.8553 (t0) REVERT: B 199 THR cc_start: 0.8883 (m) cc_final: 0.8618 (m) REVERT: B 319 LYS cc_start: 0.8464 (tptt) cc_final: 0.8227 (tmtt) REVERT: B 347 LYS cc_start: 0.7312 (tptt) cc_final: 0.6694 (tppt) REVERT: B 365 MET cc_start: 0.8138 (tmm) cc_final: 0.7672 (tmm) REVERT: B 436 LEU cc_start: 0.8819 (tp) cc_final: 0.8608 (tp) REVERT: B 556 HIS cc_start: 0.8035 (p-80) cc_final: 0.7781 (t70) REVERT: B 559 LEU cc_start: 0.9269 (mt) cc_final: 0.9038 (mt) REVERT: B 569 MET cc_start: 0.6728 (ttm) cc_final: 0.5982 (ttm) REVERT: C 37 PHE cc_start: 0.8175 (m-80) cc_final: 0.7701 (m-10) REVERT: C 53 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8630 (tppt) REVERT: C 57 ASN cc_start: 0.7467 (m110) cc_final: 0.7039 (t0) REVERT: C 65 LYS cc_start: 0.8923 (ptmt) cc_final: 0.8456 (mttt) REVERT: C 93 VAL cc_start: 0.8912 (m) cc_final: 0.8471 (p) REVERT: C 94 TYR cc_start: 0.5959 (m-80) cc_final: 0.5348 (m-80) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.2212 time to fit residues: 66.0574 Evaluate side-chains 162 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN B 481 GLN C 3 GLN C 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10400 Z= 0.185 Angle : 0.625 8.552 14111 Z= 0.306 Chirality : 0.042 0.161 1609 Planarity : 0.004 0.050 1785 Dihedral : 4.508 51.258 1483 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.96 (0.24), residues: 1276 helix: 1.60 (0.19), residues: 768 sheet: -0.02 (0.43), residues: 136 loop : -1.10 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 36 HIS 0.003 0.001 HIS B 100 PHE 0.019 0.001 PHE B 255 TYR 0.019 0.001 TYR B 187 ARG 0.004 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2552 Ramachandran restraints generated. 1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8860 (t0) cc_final: 0.8240 (t70) REVERT: A 299 TYR cc_start: 0.8688 (m-80) cc_final: 0.8249 (m-80) REVERT: A 444 PHE cc_start: 0.7019 (t80) cc_final: 0.6773 (t80) REVERT: A 445 LEU cc_start: 0.8418 (mm) cc_final: 0.7987 (tp) REVERT: B 25 LEU cc_start: 0.8751 (tp) cc_final: 0.8432 (tt) REVERT: B 79 MET cc_start: 0.8962 (tmm) cc_final: 0.8612 (tmm) REVERT: B 125 ASP cc_start: 0.7086 (m-30) cc_final: 0.6840 (m-30) REVERT: B 154 MET cc_start: 0.8844 (ttt) cc_final: 0.8518 (ttp) REVERT: B 184 ASP cc_start: 0.8812 (t70) cc_final: 0.8592 (t0) REVERT: B 199 THR cc_start: 0.8887 (m) cc_final: 0.8622 (m) REVERT: B 319 LYS cc_start: 0.8481 (tptt) cc_final: 0.8197 (tmtt) REVERT: B 347 LYS cc_start: 0.7436 (tptt) cc_final: 0.6794 (tppt) REVERT: B 365 MET cc_start: 0.8140 (tmm) cc_final: 0.7770 (tmm) REVERT: B 436 LEU cc_start: 0.8865 (tp) cc_final: 0.8500 (tp) REVERT: B 481 GLN cc_start: 0.8377 (mm110) cc_final: 0.8168 (mp10) REVERT: B 559 LEU cc_start: 0.9261 (mt) cc_final: 0.9024 (mt) REVERT: B 569 MET cc_start: 0.6790 (ttm) cc_final: 0.6044 (ttm) REVERT: C 53 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8608 (tppt) REVERT: C 57 ASN cc_start: 0.7509 (m110) cc_final: 0.7041 (t0) REVERT: C 65 LYS cc_start: 0.8944 (ptmt) cc_final: 0.8454 (mttt) REVERT: C 83 MET cc_start: 0.6953 (mmm) cc_final: 0.6617 (mmp) REVERT: C 93 VAL cc_start: 0.8876 (m) cc_final: 0.8437 (p) REVERT: C 94 TYR cc_start: 0.6056 (m-80) cc_final: 0.5481 (m-80) outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.2134 time to fit residues: 60.5930 Evaluate side-chains 151 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 103 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 HIS ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 ASN C 3 GLN C 80 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.117728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090848 restraints weight = 26475.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.092510 restraints weight = 16772.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093051 restraints weight = 12206.536| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10400 Z= 0.164 Angle : 0.616 7.849 14111 Z= 0.301 Chirality : 0.041 0.211 1609 Planarity : 0.004 0.051 1785 Dihedral : 4.461 51.975 1483 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.24), residues: 1276 helix: 1.80 (0.19), residues: 755 sheet: -0.05 (0.43), residues: 141 loop : -0.89 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 36 HIS 0.009 0.001 HIS B 111 PHE 0.021 0.001 PHE B 163 TYR 0.019 0.001 TYR B 187 ARG 0.004 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2302.79 seconds wall clock time: 42 minutes 23.38 seconds (2543.38 seconds total)