Starting phenix.real_space_refine on Tue Jun 25 05:16:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r12_14228/06_2024/7r12_14228.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r12_14228/06_2024/7r12_14228.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/7r12_14228/06_2024/7r12_14228.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r12_14228/06_2024/7r12_14228.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r12_14228/06_2024/7r12_14228.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r12_14228/06_2024/7r12_14228.pdb" } resolution = 3.3 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= 0.002 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4383 2.51 5 N 1130 2.21 5 O 1305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6858 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1972 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 14, 'TRANS': 236} Chain breaks: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.04, per 1000 atoms: 0.73 Number of scatterers: 6858 At special positions: 0 Unit cell: (75.46, 98.098, 139.062, 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 39 16.00 O 1305 8.00 N 1130 7.00 C 4383 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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 A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG D 902 " - " ASN D 53 " " NAG D 903 " - " ASN D 90 " " NAG D 904 " - " ASN D 103 " " NAG D 905 " - " ASN D 546 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 52.1% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.441A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 removed outlier: 4.067A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 removed outlier: 3.642A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.763A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.523A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.556A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.594A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 233 through 249 Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.059A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.704A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.036A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.700A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.618A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.970A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.547A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.602A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.543A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.533A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.964A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 4.081A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.622A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.617A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.216A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.696A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.862A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.525A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.752A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.199A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.287A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.643A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 301 hydrogen bonds defined for protein. 846 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.16 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2194 1.34 - 1.46: 1719 1.46 - 1.58: 3068 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 7041 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.78e+00 bond pdb=" C1 NAG D 902 " pdb=" O5 NAG D 902 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.85e+00 bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C1 NAG D 904 " pdb=" O5 NAG D 904 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 7036 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.99: 226 106.99 - 113.78: 3813 113.78 - 120.58: 2917 120.58 - 127.37: 2518 127.37 - 134.16: 92 Bond angle restraints: 9566 Sorted by residual: angle pdb=" C ASN D 90 " pdb=" N LEU D 91 " pdb=" CA LEU D 91 " ideal model delta sigma weight residual 121.54 126.61 -5.07 1.91e+00 2.74e-01 7.05e+00 angle pdb=" C LEU D 423 " pdb=" N LEU D 424 " pdb=" CA LEU D 424 " ideal model delta sigma weight residual 121.54 126.59 -5.05 1.91e+00 2.74e-01 7.00e+00 angle pdb=" CA LEU A 546 " pdb=" CB LEU A 546 " pdb=" CG LEU A 546 " ideal model delta sigma weight residual 116.30 124.89 -8.59 3.50e+00 8.16e-02 6.02e+00 angle pdb=" N ILE D 421 " pdb=" CA ILE D 421 " pdb=" C ILE D 421 " ideal model delta sigma weight residual 110.42 112.54 -2.12 9.60e-01 1.09e+00 4.87e+00 angle pdb=" N ASP D 427 " pdb=" CA ASP D 427 " pdb=" C ASP D 427 " ideal model delta sigma weight residual 110.88 108.11 2.77 1.28e+00 6.10e-01 4.68e+00 ... (remaining 9561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3824 17.55 - 35.10: 336 35.10 - 52.65: 66 52.65 - 70.20: 12 70.20 - 87.75: 4 Dihedral angle restraints: 4242 sinusoidal: 1787 harmonic: 2455 Sorted by residual: dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -119.56 33.56 1 1.00e+01 1.00e-02 1.60e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 123.28 -30.28 1 1.00e+01 1.00e-02 1.31e+01 dihedral pdb=" CA CYS D 344 " pdb=" C CYS D 344 " pdb=" N HIS D 345 " pdb=" CA HIS D 345 " ideal model delta harmonic sigma weight residual 180.00 163.88 16.12 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4239 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 604 0.030 - 0.060: 300 0.060 - 0.089: 67 0.089 - 0.119: 55 0.119 - 0.149: 6 Chirality restraints: 1032 Sorted by residual: chirality pdb=" C1 NAG D 903 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 903 " pdb=" O5 NAG D 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.54e-01 chirality pdb=" C1 NAG D 904 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D 904 " pdb=" O5 NAG D 904 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.59e-01 chirality pdb=" CA VAL A 433 " pdb=" N VAL A 433 " pdb=" C VAL A 433 " pdb=" CB VAL A 433 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1029 not shown) Planarity restraints: 1235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO D 146 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO D 235 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 578 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 579 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 579 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 579 " 0.017 5.00e-02 4.00e+02 ... (remaining 1232 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 133 2.71 - 3.26: 6429 3.26 - 3.80: 10119 3.80 - 4.35: 13356 4.35 - 4.90: 23311 Nonbonded interactions: 53348 Sorted by model distance: nonbonded pdb=" OH TYR D 183 " pdb=" OD1 ASP D 509 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU D 402 " pdb="ZN ZN D 901 " model vdw 2.211 2.230 nonbonded pdb=" O ARG A 408 " pdb=" NE2 GLN A 414 " model vdw 2.257 2.520 nonbonded pdb=" O ASP A 442 " pdb=" ND2 ASN A 448 " model vdw 2.308 2.520 nonbonded pdb=" OE1 GLU A 406 " pdb=" OH TYR A 495 " model vdw 2.325 2.440 ... (remaining 53343 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.003 0.044 7041 Z= 0.223 Angle : 0.549 8.591 9566 Z= 0.283 Chirality : 0.041 0.149 1032 Planarity : 0.004 0.050 1229 Dihedral : 13.554 87.747 2640 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.22 (0.28), residues: 374 sheet: 0.95 (0.60), residues: 70 loop : -0.81 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS D 401 PHE 0.011 0.001 PHE D 308 TYR 0.021 0.001 TYR D 199 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.720 Fit side-chains REVERT: D 160 GLU cc_start: 0.6626 (tt0) cc_final: 0.6374 (tt0) REVERT: D 470 LYS cc_start: 0.7909 (mttt) cc_final: 0.7490 (mmtm) REVERT: A 420 ASP cc_start: 0.8332 (m-30) cc_final: 0.7965 (m-30) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.1842 time to fit residues: 23.2282 Evaluate side-chains 79 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 39 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7041 Z= 0.192 Angle : 0.497 6.418 9566 Z= 0.253 Chirality : 0.041 0.149 1032 Planarity : 0.004 0.049 1229 Dihedral : 5.435 58.274 1032 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 4.74 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.68 (0.29), residues: 831 helix: 1.44 (0.28), residues: 380 sheet: 1.01 (0.60), residues: 70 loop : -0.66 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 477 HIS 0.003 0.001 HIS D 417 PHE 0.012 0.001 PHE D 327 TYR 0.020 0.001 TYR D 183 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.578 Fit side-chains REVERT: D 160 GLU cc_start: 0.6664 (tt0) cc_final: 0.6433 (tt0) REVERT: D 470 LYS cc_start: 0.7966 (mttt) cc_final: 0.7558 (mmtm) REVERT: A 405 ASP cc_start: 0.8215 (m-30) cc_final: 0.7955 (m-30) REVERT: A 420 ASP cc_start: 0.8569 (m-30) cc_final: 0.8065 (m-30) outliers start: 8 outliers final: 6 residues processed: 90 average time/residue: 0.1755 time to fit residues: 21.8064 Evaluate side-chains 86 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.0050 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7041 Z= 0.215 Angle : 0.503 6.597 9566 Z= 0.257 Chirality : 0.041 0.235 1032 Planarity : 0.004 0.048 1229 Dihedral : 4.916 57.054 1032 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.03 % Allowed : 6.09 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.67 (0.29), residues: 831 helix: 1.42 (0.28), residues: 384 sheet: 0.87 (0.60), residues: 70 loop : -0.65 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 566 HIS 0.004 0.001 HIS D 540 PHE 0.014 0.001 PHE D 327 TYR 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.746 Fit side-chains REVERT: A 420 ASP cc_start: 0.8595 (m-30) cc_final: 0.8111 (m-30) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.1658 time to fit residues: 22.7614 Evaluate side-chains 95 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.0070 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 66 optimal weight: 0.2980 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7041 Z= 0.179 Angle : 0.478 6.946 9566 Z= 0.243 Chirality : 0.041 0.231 1032 Planarity : 0.004 0.048 1229 Dihedral : 4.554 55.959 1032 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.03 % Allowed : 7.17 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.60 (0.28), residues: 378 sheet: 0.84 (0.59), residues: 70 loop : -0.50 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.010 0.001 PHE D 327 TYR 0.016 0.001 TYR D 183 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.688 Fit side-chains REVERT: D 470 LYS cc_start: 0.7956 (mttt) cc_final: 0.7571 (mmtm) REVERT: A 405 ASP cc_start: 0.8293 (m-30) cc_final: 0.7925 (m-30) REVERT: A 420 ASP cc_start: 0.8533 (m-30) cc_final: 0.8085 (m-30) outliers start: 15 outliers final: 12 residues processed: 90 average time/residue: 0.1711 time to fit residues: 21.7280 Evaluate side-chains 92 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 42 GLN D 51 ASN D 63 ASN D 175 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 7041 Z= 0.332 Angle : 0.587 11.641 9566 Z= 0.296 Chirality : 0.044 0.303 1032 Planarity : 0.004 0.050 1229 Dihedral : 4.932 57.829 1032 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.44 % Allowed : 7.98 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.48 (0.29), residues: 831 helix: 1.25 (0.28), residues: 384 sheet: 0.96 (0.60), residues: 71 loop : -0.76 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 566 HIS 0.003 0.001 HIS D 239 PHE 0.020 0.002 PHE D 327 TYR 0.016 0.002 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.681 Fit side-chains REVERT: A 420 ASP cc_start: 0.8628 (m-30) cc_final: 0.8145 (m-30) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1571 time to fit residues: 20.8865 Evaluate side-chains 91 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 7041 Z= 0.243 Angle : 0.546 14.183 9566 Z= 0.271 Chirality : 0.042 0.291 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.768 57.593 1032 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.44 % Allowed : 9.34 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.63 (0.29), residues: 831 helix: 1.40 (0.28), residues: 380 sheet: 1.09 (0.61), residues: 71 loop : -0.72 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.013 0.001 PHE D 327 TYR 0.015 0.001 TYR D 183 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.705 Fit side-chains REVERT: A 420 ASP cc_start: 0.8610 (m-30) cc_final: 0.8150 (m-30) REVERT: A 546 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7685 (pt) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1611 time to fit residues: 21.3183 Evaluate side-chains 93 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 79 optimal weight: 0.0060 chunk 50 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 0.4980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 175 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 7041 Z= 0.165 Angle : 0.485 11.713 9566 Z= 0.243 Chirality : 0.040 0.243 1032 Planarity : 0.003 0.049 1229 Dihedral : 4.442 56.610 1032 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.03 % Allowed : 10.69 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.94 (0.29), residues: 831 helix: 1.65 (0.28), residues: 378 sheet: 1.25 (0.62), residues: 71 loop : -0.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS D 540 PHE 0.007 0.001 PHE D 327 TYR 0.015 0.001 TYR D 50 ARG 0.001 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.686 Fit side-chains REVERT: D 470 LYS cc_start: 0.7911 (mttt) cc_final: 0.7507 (mmtm) REVERT: D 568 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8078 (tt) REVERT: A 420 ASP cc_start: 0.8536 (m-30) cc_final: 0.8086 (m-30) outliers start: 15 outliers final: 12 residues processed: 94 average time/residue: 0.1676 time to fit residues: 22.0542 Evaluate side-chains 97 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.0770 chunk 7 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.0670 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 7041 Z= 0.218 Angle : 0.530 14.220 9566 Z= 0.264 Chirality : 0.041 0.262 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.584 57.539 1032 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 10.96 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.29), residues: 831 helix: 1.62 (0.28), residues: 377 sheet: 1.25 (0.62), residues: 71 loop : -0.57 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.013 0.001 PHE D 327 TYR 0.021 0.001 TYR D 50 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.732 Fit side-chains REVERT: D 568 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8073 (tt) REVERT: A 420 ASP cc_start: 0.8569 (m-30) cc_final: 0.8104 (m-30) REVERT: A 546 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7626 (pt) outliers start: 17 outliers final: 12 residues processed: 93 average time/residue: 0.1600 time to fit residues: 21.0039 Evaluate side-chains 96 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 58 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 7041 Z= 0.193 Angle : 0.512 13.526 9566 Z= 0.254 Chirality : 0.041 0.244 1032 Planarity : 0.004 0.048 1229 Dihedral : 4.529 57.625 1032 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.30 % Allowed : 10.96 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.93 (0.29), residues: 831 helix: 1.65 (0.28), residues: 378 sheet: 1.22 (0.63), residues: 70 loop : -0.53 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 566 HIS 0.003 0.001 HIS D 540 PHE 0.011 0.001 PHE D 327 TYR 0.018 0.001 TYR D 50 ARG 0.001 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 84 time to evaluate : 0.833 Fit side-chains REVERT: D 568 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8096 (tt) REVERT: A 420 ASP cc_start: 0.8579 (m-30) cc_final: 0.8127 (m-30) REVERT: A 546 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (pt) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.1685 time to fit residues: 22.5347 Evaluate side-chains 98 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.4980 chunk 82 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.0470 chunk 52 optimal weight: 0.2980 chunk 70 optimal weight: 0.0370 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 7041 Z= 0.161 Angle : 0.488 13.197 9566 Z= 0.242 Chirality : 0.040 0.229 1032 Planarity : 0.003 0.048 1229 Dihedral : 4.359 56.465 1032 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.89 % Allowed : 11.23 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.30), residues: 831 helix: 1.78 (0.28), residues: 378 sheet: 1.07 (0.57), residues: 80 loop : -0.43 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS D 540 PHE 0.009 0.001 PHE D 308 TYR 0.018 0.001 TYR D 50 ARG 0.001 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.690 Fit side-chains REVERT: D 568 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 420 ASP cc_start: 0.8539 (m-30) cc_final: 0.8105 (m-30) REVERT: A 546 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7497 (pt) outliers start: 14 outliers final: 12 residues processed: 92 average time/residue: 0.1652 time to fit residues: 21.5181 Evaluate side-chains 92 residues out of total 739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 496 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.161634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.148017 restraints weight = 7169.096| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 0.62 r_work: 0.3170 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7041 Z= 0.302 Angle : 0.583 13.591 9566 Z= 0.289 Chirality : 0.043 0.255 1032 Planarity : 0.004 0.049 1229 Dihedral : 4.781 58.736 1032 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.17 % Allowed : 10.83 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.70 (0.29), residues: 831 helix: 1.44 (0.28), residues: 383 sheet: 1.18 (0.63), residues: 70 loop : -0.67 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS D 239 PHE 0.017 0.002 PHE D 327 TYR 0.016 0.002 TYR D 385 ARG 0.003 0.000 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.16 seconds wall clock time: 32 minutes 19.73 seconds (1939.73 seconds total)