Starting phenix.real_space_refine (version: dev) on Mon Feb 20 12:35:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/02_2023/7zrd_14911_updated.pdb" } resolution = 3.3 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1080 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D GLU 27": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11037 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' K': 2, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.00, per 1000 atoms: 0.63 Number of scatterers: 11037 At special positions: 0 Unit cell: (88.044, 112.332, 142.692, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 1 22.97 K 9 19.00 S 62 16.00 P 5 15.00 O 2002 8.00 N 1823 7.00 C 7135 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: 4.94 Conformation dependent library (CDL) restraints added in 1.8 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 6 sheets defined 55.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.662A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.612A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.769A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.398A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 303 removed outlier: 3.595A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.704A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 380 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.633A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.552A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.601A pdb=" N ASP C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 19 removed outlier: 4.000A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 64 through 101 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 216 through 246 removed outlier: 3.946A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.946A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 284 removed outlier: 5.871A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.719A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.726A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.655A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 539 through 542 No H-bonds generated for 'chain 'B' and resid 539 through 542' Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.148A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 566 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 570 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 575 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.805A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.152A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.231A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.631A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 188 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.556A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 167 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 548 through 550 removed outlier: 3.653A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.577A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.907A pdb=" N THR B 429 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 444 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1536 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: 3.47 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3520 1.34 - 1.49: 2621 1.49 - 1.63: 4969 1.63 - 1.77: 1 1.77 - 1.91: 115 Bond restraints: 11226 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.78e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.77e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.38e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.50e-02 4.44e+03 4.29e+00 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.48: 210 104.48 - 111.89: 5390 111.89 - 119.31: 4075 119.31 - 126.72: 5400 126.72 - 134.14: 158 Bond angle restraints: 15233 Sorted by residual: angle pdb=" C LEU A 261 " pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 120.24 122.82 -2.58 6.30e-01 2.52e+00 1.68e+01 angle pdb=" C PRO C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ASN B 547 " pdb=" N MET B 548 " pdb=" CA MET B 548 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N VAL B 664 " pdb=" CA VAL B 664 " pdb=" C VAL B 664 " ideal model delta sigma weight residual 108.88 116.65 -7.77 2.16e+00 2.14e-01 1.29e+01 angle pdb=" C ALA B 210 " pdb=" N GLN B 211 " pdb=" CA GLN B 211 " ideal model delta sigma weight residual 122.08 127.11 -5.03 1.47e+00 4.63e-01 1.17e+01 ... (remaining 15228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5887 17.41 - 34.82: 617 34.82 - 52.22: 150 52.22 - 69.63: 38 69.63 - 87.04: 11 Dihedral angle restraints: 6703 sinusoidal: 2591 harmonic: 4112 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LEU B 183 " pdb=" C LEU B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 34 " pdb=" C PHE C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1420 0.055 - 0.109: 331 0.109 - 0.164: 55 0.164 - 0.218: 5 0.218 - 0.273: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL B 14 " pdb=" CA VAL B 14 " pdb=" CG1 VAL B 14 " pdb=" CG2 VAL B 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1811 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 323 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO B 324 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 429 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 430 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 362 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.029 5.00e-02 4.00e+02 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 3614 2.85 - 3.42: 12278 3.42 - 3.99: 21772 3.99 - 4.57: 30998 4.57 - 5.14: 44521 Nonbonded interactions: 113183 Sorted by model distance: nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.272 2.440 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.283 2.440 nonbonded pdb=" O GLN B 422 " pdb=" OE1 GLN B 426 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 462 " pdb=" O SER A 469 " model vdw 2.315 2.440 ... (remaining 113178 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: 7 Type Number sf(0) Gaussians K 9 8.98 5 V 1 8.30 5 P 5 5.49 5 S 62 5.16 5 C 7135 2.51 5 N 1823 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.150 Process input model: 32.600 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.004 0.066 11226 Z= 0.287 Angle : 0.809 10.413 15233 Z= 0.413 Chirality : 0.048 0.273 1814 Planarity : 0.006 0.123 1912 Dihedral : 15.862 87.042 4061 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.00 % 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: -0.83 (0.20), residues: 1441 helix: -0.14 (0.16), residues: 856 sheet: -0.24 (0.64), residues: 76 loop : -1.13 (0.26), residues: 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.441 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2252 time to fit residues: 50.4900 Evaluate side-chains 122 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 0.0670 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 ASN ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 80 GLN B 217 ASN B 390 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11226 Z= 0.283 Angle : 0.541 6.860 15233 Z= 0.276 Chirality : 0.040 0.150 1814 Planarity : 0.005 0.077 1912 Dihedral : 10.290 59.828 1677 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 1.06 % 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: 0.13 (0.22), residues: 1441 helix: 0.78 (0.17), residues: 856 sheet: -0.28 (0.61), residues: 81 loop : -0.96 (0.27), residues: 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.279 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 133 average time/residue: 0.2257 time to fit residues: 44.6442 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 112 time to evaluate : 1.206 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1065 time to fit residues: 3.4712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11226 Z= 0.164 Angle : 0.477 7.122 15233 Z= 0.241 Chirality : 0.038 0.153 1814 Planarity : 0.004 0.063 1912 Dihedral : 9.655 59.597 1677 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.70 % 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: 0.52 (0.22), residues: 1441 helix: 1.17 (0.18), residues: 857 sheet: -0.36 (0.60), residues: 83 loop : -0.89 (0.27), residues: 501 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.319 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 0.2230 time to fit residues: 41.7048 Evaluate side-chains 122 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 1.183 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1207 time to fit residues: 3.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.160 Angle : 0.462 7.046 15233 Z= 0.233 Chirality : 0.038 0.153 1814 Planarity : 0.004 0.055 1912 Dihedral : 9.151 59.675 1677 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer Outliers : 0.88 % 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: 0.86 (0.22), residues: 1441 helix: 1.45 (0.18), residues: 851 sheet: -0.36 (0.59), residues: 83 loop : -0.73 (0.28), residues: 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 1.193 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 129 average time/residue: 0.2251 time to fit residues: 43.4498 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1184 time to fit residues: 3.2349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.140 Angle : 0.449 7.110 15233 Z= 0.227 Chirality : 0.038 0.162 1814 Planarity : 0.003 0.050 1912 Dihedral : 8.800 59.412 1677 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.88 % 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: 1.09 (0.23), residues: 1441 helix: 1.67 (0.18), residues: 843 sheet: -0.28 (0.60), residues: 83 loop : -0.67 (0.27), residues: 515 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 1.234 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 131 average time/residue: 0.2207 time to fit residues: 43.2807 Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.359 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1216 time to fit residues: 3.3703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11226 Z= 0.163 Angle : 0.461 7.096 15233 Z= 0.231 Chirality : 0.038 0.153 1814 Planarity : 0.003 0.049 1912 Dihedral : 8.430 59.158 1677 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.70 % 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: 1.10 (0.23), residues: 1441 helix: 1.67 (0.18), residues: 844 sheet: -0.22 (0.60), residues: 83 loop : -0.65 (0.28), residues: 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 1.283 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 0.2306 time to fit residues: 43.1947 Evaluate side-chains 124 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1766 time to fit residues: 3.4289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.160 Angle : 0.463 7.039 15233 Z= 0.232 Chirality : 0.038 0.135 1814 Planarity : 0.003 0.047 1912 Dihedral : 8.111 59.949 1677 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.79 % 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: 1.14 (0.23), residues: 1441 helix: 1.71 (0.18), residues: 844 sheet: -0.25 (0.60), residues: 83 loop : -0.64 (0.28), residues: 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 1.331 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 129 average time/residue: 0.2256 time to fit residues: 43.4062 Evaluate side-chains 124 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.239 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1108 time to fit residues: 2.8861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.0070 chunk 82 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 40.0000 chunk 93 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.149 Angle : 0.469 7.096 15233 Z= 0.234 Chirality : 0.038 0.175 1814 Planarity : 0.003 0.045 1912 Dihedral : 7.926 57.088 1677 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 0.26 % 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 (0.23), residues: 1441 helix: 1.76 (0.18), residues: 843 sheet: -0.22 (0.60), residues: 83 loop : -0.62 (0.28), residues: 515 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 1.304 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 121 average time/residue: 0.2413 time to fit residues: 43.2222 Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 116 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1281 time to fit residues: 2.2301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN A 523 HIS C 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 11226 Z= 0.323 Angle : 0.550 7.220 15233 Z= 0.276 Chirality : 0.041 0.200 1814 Planarity : 0.004 0.054 1912 Dihedral : 8.298 59.805 1677 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.62 % 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: 0.76 (0.22), residues: 1441 helix: 1.31 (0.18), residues: 852 sheet: -0.24 (0.59), residues: 81 loop : -0.67 (0.28), residues: 508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 114 time to evaluate : 1.359 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 116 average time/residue: 0.2401 time to fit residues: 42.1078 Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1207 time to fit residues: 2.7334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.0980 chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 142 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.161 Angle : 0.480 7.016 15233 Z= 0.241 Chirality : 0.038 0.134 1814 Planarity : 0.003 0.045 1912 Dihedral : 7.855 59.147 1677 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.44 % 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: 1.03 (0.23), residues: 1441 helix: 1.54 (0.18), residues: 851 sheet: -0.22 (0.61), residues: 83 loop : -0.57 (0.28), residues: 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.296 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 120 average time/residue: 0.2314 time to fit residues: 41.8749 Evaluate side-chains 114 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 112 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1228 time to fit residues: 2.2051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 0.2980 chunk 116 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 0.0970 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.131254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.100111 restraints weight = 13929.988| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.20 r_work: 0.2951 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11226 Z= 0.243 Angle : 0.518 7.076 15233 Z= 0.259 Chirality : 0.040 0.157 1814 Planarity : 0.004 0.044 1912 Dihedral : 7.855 58.371 1677 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.18 % 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: 0.91 (0.23), residues: 1441 helix: 1.43 (0.18), residues: 852 sheet: -0.30 (0.60), residues: 83 loop : -0.58 (0.28), residues: 506 =============================================================================== Job complete usr+sys time: 2230.81 seconds wall clock time: 41 minutes 49.83 seconds (2509.83 seconds total)