Starting phenix.real_space_refine on Thu Mar 14 20:10:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yv8_34120/03_2024/7yv8_34120.pdb" } resolution = 2.94 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= 0.000 sd= 0.012 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 3164 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 4163 2.51 5 N 1077 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A ASP 292": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A ASP 609": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6513 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "B" Number of atoms: 1574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1574 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 12, 'TRANS': 184} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.07, per 1000 atoms: 0.62 Number of scatterers: 6513 At special positions: 0 Unit cell: (73.92, 102.08, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1236 8.00 N 1077 7.00 C 4163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 53 " " NAG A 704 " - " ASN A 82 " " NAG A 705 " - " ASN A 432 " " NAG A 706 " - " ASN A 546 " " NAG B 601 " - " ASN B 343 " Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 7 sheets defined 55.1% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.752A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.685A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.520A pdb=" N ALA A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 100 " --> pdb=" O GLN A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.871A pdb=" N ASP A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.536A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.628A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.990A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.635A pdb=" N MET A 249 " --> pdb=" O ARG A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.719A pdb=" N TYR A 255 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 256' Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.534A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.829A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.738A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.737A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.954A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.546A pdb=" N ASN A 508 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP A 509 " --> pdb=" O VAL A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 513 through 532 removed outlier: 4.119A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.657A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.808A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.714A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.550A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 removed outlier: 3.872A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.812A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.964A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.255A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.635A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'B' and resid 473 through 474 281 hydrogen bonds defined for protein. 783 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: 1.93 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2102 1.35 - 1.49: 1857 1.49 - 1.62: 2677 1.62 - 1.75: 0 1.75 - 1.88: 56 Bond restraints: 6692 Sorted by residual: bond pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 1.808 1.883 -0.075 3.30e-02 9.18e+02 5.10e+00 bond pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta sigma weight residual 1.456 1.477 -0.021 1.26e-02 6.30e+03 2.89e+00 bond pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 1.808 1.754 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" C1 NAG A 704 " pdb=" O5 NAG A 704 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG A 705 " pdb=" O5 NAG A 705 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.95e+00 ... (remaining 6687 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.56: 202 106.56 - 113.46: 3475 113.46 - 120.35: 2612 120.35 - 127.24: 2712 127.24 - 134.13: 92 Bond angle restraints: 9093 Sorted by residual: angle pdb=" CA CYS B 379 " pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " ideal model delta sigma weight residual 114.40 129.26 -14.86 2.30e+00 1.89e-01 4.18e+01 angle pdb=" C LYS B 378 " pdb=" N CYS B 379 " pdb=" CA CYS B 379 " ideal model delta sigma weight residual 121.62 114.59 7.03 1.83e+00 2.99e-01 1.48e+01 angle pdb=" N CYS B 379 " pdb=" CA CYS B 379 " pdb=" C CYS B 379 " ideal model delta sigma weight residual 108.79 114.23 -5.44 1.53e+00 4.27e-01 1.27e+01 angle pdb=" N THR B 500 " pdb=" CA THR B 500 " pdb=" CB THR B 500 " ideal model delta sigma weight residual 110.56 106.86 3.70 1.46e+00 4.69e-01 6.42e+00 angle pdb=" N ASN B 388 " pdb=" CA ASN B 388 " pdb=" C ASN B 388 " ideal model delta sigma weight residual 110.80 105.51 5.29 2.13e+00 2.20e-01 6.16e+00 ... (remaining 9088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 3700 21.44 - 42.88: 284 42.88 - 64.32: 33 64.32 - 85.76: 12 85.76 - 107.20: 9 Dihedral angle restraints: 4038 sinusoidal: 1710 harmonic: 2328 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 -179.03 -87.97 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 35.02 57.98 1 1.00e+01 1.00e-02 4.51e+01 ... (remaining 4035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 641 0.042 - 0.084: 249 0.084 - 0.126: 69 0.126 - 0.168: 4 0.168 - 0.210: 1 Chirality restraints: 964 Sorted by residual: chirality pdb=" CA CYS B 379 " pdb=" N CYS B 379 " pdb=" C CYS B 379 " pdb=" CB CYS B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" C PRO B 491 " pdb=" CB PRO B 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA ILE B 434 " pdb=" N ILE B 434 " pdb=" C ILE B 434 " pdb=" CB ILE B 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 961 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 388 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C ASN B 388 " -0.032 2.00e-02 2.50e+03 pdb=" O ASN B 388 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 389 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 65 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ALA A 65 " 0.031 2.00e-02 2.50e+03 pdb=" O ALA A 65 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA A 66 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 481 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ASN B 481 " -0.031 2.00e-02 2.50e+03 pdb=" O ASN B 481 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 482 " 0.010 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 30 2.58 - 3.16: 5204 3.16 - 3.74: 9136 3.74 - 4.32: 12960 4.32 - 4.90: 22350 Nonbonded interactions: 49680 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 2.006 2.230 nonbonded pdb=" O ASN B 481 " pdb=" ND2 ASN B 481 " model vdw 2.234 2.520 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.239 2.440 nonbonded pdb=" OE2 GLU A 57 " pdb=" O6 NAG A 703 " model vdw 2.281 2.440 nonbonded pdb=" OG1 THR A 365 " pdb=" OD1 ASP A 367 " model vdw 2.298 2.440 ... (remaining 49675 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 26.180 Check model and map are aligned: 0.120 Set scattering table: 0.060 Process input model: 22.990 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.005 0.075 6692 Z= 0.326 Angle : 0.652 14.865 9093 Z= 0.340 Chirality : 0.045 0.210 964 Planarity : 0.005 0.041 1174 Dihedral : 15.362 107.195 2525 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.15 % Allowed : 0.29 % Favored : 99.56 % 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: -0.89 (0.30), residues: 789 helix: 0.07 (0.29), residues: 368 sheet: 2.02 (0.95), residues: 34 loop : -1.48 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE B 377 TYR 0.024 0.002 TYR A 199 ARG 0.005 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 0.737 Fit side-chains REVERT: A 42 GLN cc_start: 0.7959 (mt0) cc_final: 0.7613 (mt0) REVERT: A 190 MET cc_start: 0.7969 (tmm) cc_final: 0.7633 (tmt) REVERT: A 375 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7273 (mm-30) REVERT: B 340 GLU cc_start: 0.6942 (mp0) cc_final: 0.6610 (mp0) outliers start: 1 outliers final: 0 residues processed: 151 average time/residue: 1.2111 time to fit residues: 191.6428 Evaluate side-chains 134 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 37 optimal weight: 0.0050 chunk 45 optimal weight: 0.2980 chunk 70 optimal weight: 0.1980 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 HIS B 360 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 6692 Z= 0.200 Angle : 0.583 14.005 9093 Z= 0.289 Chirality : 0.043 0.214 964 Planarity : 0.004 0.043 1174 Dihedral : 6.465 59.730 992 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.02 % Allowed : 8.56 % Favored : 90.42 % 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: -0.15 (0.31), residues: 789 helix: 0.82 (0.29), residues: 372 sheet: 1.70 (0.81), residues: 44 loop : -1.30 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 512 TYR 0.012 0.001 TYR A 199 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.727 Fit side-chains REVERT: A 190 MET cc_start: 0.7898 (tmm) cc_final: 0.7609 (tmt) REVERT: A 375 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7407 (mm-30) REVERT: A 408 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6758 (mmm) REVERT: B 340 GLU cc_start: 0.7034 (mp0) cc_final: 0.6646 (mp0) outliers start: 7 outliers final: 3 residues processed: 140 average time/residue: 1.1747 time to fit residues: 172.6991 Evaluate side-chains 137 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.0370 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 53 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6692 Z= 0.305 Angle : 0.609 12.307 9093 Z= 0.304 Chirality : 0.045 0.231 964 Planarity : 0.004 0.045 1174 Dihedral : 5.625 56.844 992 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.89 % Allowed : 10.01 % Favored : 88.10 % 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: -0.11 (0.31), residues: 789 helix: 0.97 (0.29), residues: 373 sheet: 2.00 (0.92), residues: 34 loop : -1.36 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.002 PHE A 327 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 42 GLN cc_start: 0.7971 (mt0) cc_final: 0.7625 (mt0) REVERT: A 190 MET cc_start: 0.7890 (tmm) cc_final: 0.7598 (tmt) REVERT: A 375 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7395 (mm-30) REVERT: A 401 HIS cc_start: 0.8589 (OUTLIER) cc_final: 0.8105 (m-70) REVERT: A 408 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6867 (mmm) REVERT: B 340 GLU cc_start: 0.7116 (mp0) cc_final: 0.6688 (mp0) outliers start: 13 outliers final: 5 residues processed: 139 average time/residue: 1.1973 time to fit residues: 174.6954 Evaluate side-chains 138 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0980 chunk 7 optimal weight: 0.0050 chunk 33 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 0.0670 chunk 67 optimal weight: 0.0570 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 overall best weight: 0.0568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 6692 Z= 0.143 Angle : 0.520 13.029 9093 Z= 0.257 Chirality : 0.041 0.218 964 Planarity : 0.004 0.045 1174 Dihedral : 5.122 55.565 992 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.02 % Allowed : 11.90 % Favored : 87.08 % 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: 0.39 (0.31), residues: 789 helix: 1.54 (0.29), residues: 366 sheet: 1.64 (0.80), residues: 44 loop : -1.26 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.002 0.001 HIS A 374 PHE 0.006 0.001 PHE A 315 TYR 0.008 0.001 TYR B 380 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 0.770 Fit side-chains REVERT: A 190 MET cc_start: 0.7753 (tmm) cc_final: 0.7478 (tmt) REVERT: B 340 GLU cc_start: 0.7137 (mp0) cc_final: 0.6643 (mp0) REVERT: B 374 PHE cc_start: 0.7847 (m-10) cc_final: 0.7512 (m-80) REVERT: B 438 SER cc_start: 0.7733 (p) cc_final: 0.7318 (p) outliers start: 7 outliers final: 2 residues processed: 150 average time/residue: 1.1739 time to fit residues: 184.7651 Evaluate side-chains 142 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6692 Z= 0.241 Angle : 0.577 11.231 9093 Z= 0.284 Chirality : 0.042 0.211 964 Planarity : 0.004 0.045 1174 Dihedral : 5.162 53.660 992 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.89 % Allowed : 13.64 % Favored : 84.47 % 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: 0.41 (0.31), residues: 789 helix: 1.56 (0.29), residues: 366 sheet: 1.61 (0.81), residues: 44 loop : -1.25 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.014 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 0.780 Fit side-chains REVERT: A 190 MET cc_start: 0.7840 (tmm) cc_final: 0.7558 (tmt) REVERT: B 340 GLU cc_start: 0.7152 (mp0) cc_final: 0.6655 (mp0) REVERT: B 374 PHE cc_start: 0.7918 (m-10) cc_final: 0.7544 (m-80) outliers start: 13 outliers final: 5 residues processed: 150 average time/residue: 1.2120 time to fit residues: 190.9901 Evaluate side-chains 142 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 34 optimal weight: 0.0370 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6692 Z= 0.251 Angle : 0.581 13.622 9093 Z= 0.288 Chirality : 0.043 0.230 964 Planarity : 0.004 0.046 1174 Dihedral : 5.221 54.150 992 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.89 % Allowed : 15.09 % Favored : 83.02 % 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: 0.39 (0.31), residues: 789 helix: 1.55 (0.29), residues: 365 sheet: 1.64 (0.81), residues: 44 loop : -1.26 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.013 0.001 TYR A 385 ARG 0.003 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7841 (tmm) cc_final: 0.7563 (tmt) REVERT: B 340 GLU cc_start: 0.7157 (mp0) cc_final: 0.6644 (mp0) REVERT: B 374 PHE cc_start: 0.7896 (m-10) cc_final: 0.7536 (m-80) outliers start: 13 outliers final: 7 residues processed: 142 average time/residue: 1.1645 time to fit residues: 173.6782 Evaluate side-chains 143 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 0.3980 chunk 75 optimal weight: 0.0050 chunk 47 optimal weight: 0.0770 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 6692 Z= 0.213 Angle : 0.565 12.904 9093 Z= 0.279 Chirality : 0.042 0.224 964 Planarity : 0.004 0.045 1174 Dihedral : 5.105 54.195 992 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.60 % Allowed : 15.82 % Favored : 82.58 % 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: 0.49 (0.31), residues: 789 helix: 1.65 (0.29), residues: 365 sheet: 1.59 (0.81), residues: 44 loop : -1.21 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.011 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7852 (tmm) cc_final: 0.7569 (tmt) REVERT: B 340 GLU cc_start: 0.7165 (mp0) cc_final: 0.6645 (mp0) REVERT: B 374 PHE cc_start: 0.7890 (m-10) cc_final: 0.7574 (m-80) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 1.1461 time to fit residues: 174.8862 Evaluate side-chains 144 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 65 optimal weight: 0.0770 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 481 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 6692 Z= 0.282 Angle : 0.606 12.707 9093 Z= 0.301 Chirality : 0.044 0.230 964 Planarity : 0.004 0.045 1174 Dihedral : 5.191 53.884 992 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.60 % Allowed : 16.40 % Favored : 82.00 % 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: 0.33 (0.31), residues: 789 helix: 1.57 (0.29), residues: 364 sheet: 1.93 (0.95), residues: 34 loop : -1.31 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE A 327 TYR 0.014 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7854 (tmm) cc_final: 0.7577 (OUTLIER) REVERT: B 340 GLU cc_start: 0.7167 (mp0) cc_final: 0.6638 (mp0) REVERT: B 374 PHE cc_start: 0.7899 (m-10) cc_final: 0.7556 (m-80) outliers start: 11 outliers final: 8 residues processed: 142 average time/residue: 1.1872 time to fit residues: 176.8682 Evaluate side-chains 145 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 66 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.0170 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 6692 Z= 0.251 Angle : 0.601 14.068 9093 Z= 0.298 Chirality : 0.043 0.225 964 Planarity : 0.004 0.044 1174 Dihedral : 5.170 53.994 992 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.45 % Allowed : 16.55 % Favored : 82.00 % 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: 0.38 (0.31), residues: 789 helix: 1.57 (0.29), residues: 365 sheet: 2.07 (0.96), residues: 34 loop : -1.26 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7856 (tmm) cc_final: 0.7579 (tmt) REVERT: B 340 GLU cc_start: 0.7168 (mp0) cc_final: 0.6641 (mp0) REVERT: B 374 PHE cc_start: 0.7885 (m-10) cc_final: 0.7536 (m-80) outliers start: 10 outliers final: 8 residues processed: 142 average time/residue: 1.1798 time to fit residues: 175.8850 Evaluate side-chains 144 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 0.1980 chunk 57 optimal weight: 0.3980 chunk 9 optimal weight: 0.0010 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6692 Z= 0.241 Angle : 0.599 13.918 9093 Z= 0.299 Chirality : 0.043 0.220 964 Planarity : 0.004 0.045 1174 Dihedral : 5.126 53.819 992 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.31 % Allowed : 17.13 % Favored : 81.57 % 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: 0.40 (0.31), residues: 789 helix: 1.60 (0.29), residues: 365 sheet: 2.10 (0.96), residues: 34 loop : -1.27 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 135 time to evaluate : 0.677 Fit side-chains REVERT: A 190 MET cc_start: 0.7852 (tmm) cc_final: 0.7573 (tmt) REVERT: B 340 GLU cc_start: 0.7170 (mp0) cc_final: 0.6645 (mp0) REVERT: B 374 PHE cc_start: 0.7872 (m-10) cc_final: 0.7513 (m-80) REVERT: B 420 ASP cc_start: 0.7494 (m-30) cc_final: 0.7092 (m-30) outliers start: 9 outliers final: 8 residues processed: 139 average time/residue: 1.2139 time to fit residues: 177.1329 Evaluate side-chains 144 residues out of total 689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 136 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 63 optimal weight: 0.4980 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 70 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095234 restraints weight = 9427.022| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.83 r_work: 0.3106 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6692 Z= 0.246 Angle : 0.611 13.899 9093 Z= 0.302 Chirality : 0.043 0.218 964 Planarity : 0.004 0.045 1174 Dihedral : 5.121 53.824 992 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 1.16 % Allowed : 17.27 % Favored : 81.57 % 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: 0.42 (0.31), residues: 789 helix: 1.60 (0.29), residues: 365 sheet: 2.10 (0.96), residues: 34 loop : -1.24 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3604.86 seconds wall clock time: 64 minutes 1.61 seconds (3841.61 seconds total)