Starting phenix.real_space_refine (version: dev) on Fri Feb 17 22:53:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo6_33338/02_2023/7xo6_33338.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Process input model Symmetric amino acids flipped Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 406": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D GLU 597": "OE1" <-> "OE2" Residue "D ARG 600": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6440 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 Chain: "A" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1559 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" 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 chiralities: 2 Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" 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 chiralities: 1 Time building chain proxies: 4.41, per 1000 atoms: 0.68 Number of scatterers: 6440 At special positions: 0 Unit cell: (97.232, 74.984, 121.952, 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 37 16.00 O 1214 8.00 N 1076 7.00 C 4112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG B 1 " - " ASN D 53 " " NAG D 902 " - " ASN D 546 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 994.4 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1486 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 6 sheets defined 56.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'D' and resid 22 through 53 removed outlier: 4.023A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.671A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.705A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.964A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.922A 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 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 250 removed outlier: 3.769A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.521A pdb=" N ARG D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.626A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.653A 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 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.637A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 446 removed outlier: 3.516A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 465 removed outlier: 4.468A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 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: 3.719A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.514A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.514A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 343' Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.705A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.265A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing sheet with id=AA1, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.858A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.935A 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 354 through 357 removed outlier: 3.798A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.595A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 831 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: 1.77 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1188 1.33 - 1.45: 1836 1.45 - 1.57: 3536 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6618 Sorted by residual: bond pdb=" CA SER A 349 " pdb=" CB SER A 349 " ideal model delta sigma weight residual 1.529 1.458 0.071 1.61e-02 3.86e+03 1.93e+01 bond pdb=" C ALA A 348 " pdb=" N SER A 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.31e-02 5.83e+03 6.32e+00 bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.435 1.408 0.027 1.10e-02 8.26e+03 6.22e+00 bond pdb=" CA ALA A 348 " pdb=" CB ALA A 348 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.66e-02 3.63e+03 5.69e+00 bond pdb=" C PRO A 373 " pdb=" O PRO A 373 " ideal model delta sigma weight residual 1.235 1.206 0.029 1.30e-02 5.92e+03 4.91e+00 ... (remaining 6613 not shown) Histogram of bond angle deviations from ideal: 98.76 - 105.81: 142 105.81 - 112.86: 3388 112.86 - 119.90: 2267 119.90 - 126.95: 3084 126.95 - 134.00: 106 Bond angle restraints: 8987 Sorted by residual: angle pdb=" C3 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" N2 NAG B 1 " ideal model delta sigma weight residual 110.58 98.76 11.82 9.20e-01 1.18e+00 1.65e+02 angle pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 109.64 103.32 6.32 5.38e-01 3.45e+00 1.38e+02 angle pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 109.64 112.51 -2.87 5.38e-01 3.45e+00 2.85e+01 angle pdb=" C1 NAG A1301 " pdb=" C2 NAG A1301 " pdb=" C3 NAG A1301 " ideal model delta sigma weight residual 110.19 105.32 4.87 9.25e-01 1.17e+00 2.77e+01 angle pdb=" C1 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" N2 NAG B 1 " ideal model delta sigma weight residual 111.03 104.66 6.37 1.25e+00 6.40e-01 2.60e+01 ... (remaining 8982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3575 17.64 - 35.29: 243 35.29 - 52.93: 47 52.93 - 70.57: 15 70.57 - 88.22: 8 Dihedral angle restraints: 3888 sinusoidal: 1575 harmonic: 2313 Sorted by residual: dihedral pdb=" C ASP A 339 " pdb=" N ASP A 339 " pdb=" CA ASP A 339 " pdb=" CB ASP A 339 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" C GLN D 287 " pdb=" N GLN D 287 " pdb=" CA GLN D 287 " pdb=" CB GLN D 287 " ideal model delta harmonic sigma weight residual -122.60 -131.90 9.30 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PRO D 289 " pdb=" C PRO D 289 " pdb=" CA PRO D 289 " pdb=" CB PRO D 289 " ideal model delta harmonic sigma weight residual 115.10 124.08 -8.98 0 2.50e+00 1.60e-01 1.29e+01 ... (remaining 3885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 940 0.338 - 0.675: 4 0.675 - 1.013: 0 1.013 - 1.350: 1 1.350 - 1.688: 1 Chirality restraints: 946 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.19e+01 chirality pdb=" CG LEU A 518 " pdb=" CB LEU A 518 " pdb=" CD1 LEU A 518 " pdb=" CD2 LEU A 518 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 943 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.266 2.00e-02 2.50e+03 2.22e-01 6.14e+02 pdb=" C7 NAG A1301 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.369 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.189 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG B 2 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.240 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 902 " 0.159 2.00e-02 2.50e+03 1.33e-01 2.22e+02 pdb=" C7 NAG D 902 " -0.044 2.00e-02 2.50e+03 pdb=" C8 NAG D 902 " 0.117 2.00e-02 2.50e+03 pdb=" N2 NAG D 902 " -0.218 2.00e-02 2.50e+03 pdb=" O7 NAG D 902 " -0.014 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 80 2.64 - 3.21: 5947 3.21 - 3.77: 10011 3.77 - 4.34: 13887 4.34 - 4.90: 23217 Nonbonded interactions: 53142 Sorted by model distance: nonbonded pdb=" OH TYR D 279 " pdb=" OD1 ASN D 290 " model vdw 2.075 2.440 nonbonded pdb=" OG1 THR D 365 " pdb=" OD1 ASN D 368 " model vdw 2.146 2.440 nonbonded pdb=" OD2 ASP D 494 " pdb=" OG1 THR D 496 " model vdw 2.156 2.440 nonbonded pdb=" NH1 ARG D 177 " pdb=" O GLU D 495 " model vdw 2.221 2.520 nonbonded pdb=" O ALA D 212 " pdb=" ND2 ASN D 216 " model vdw 2.269 2.520 ... (remaining 53137 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4112 2.51 5 N 1076 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 22.040 Check model and map are aligned: 0.120 Process input model: 20.660 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:14.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 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 0.071 6618 Z= 0.162 Angle : 0.550 11.820 8987 Z= 0.376 Chirality : 0.079 1.688 946 Planarity : 0.009 0.222 1160 Dihedral : 13.218 88.216 2402 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.28), residues: 780 helix: -0.11 (0.25), residues: 385 sheet: -0.50 (0.74), residues: 41 loop : -1.95 (0.30), residues: 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.688 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 212 average time/residue: 1.1449 time to fit residues: 255.3598 Evaluate side-chains 156 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0412 ------------------------------------------------------------------------------- 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: 0.3980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 86 GLN D 101 GLN D 102 GLN D 197 ASN D 221 GLN D 265 HIS D 373 HIS D 378 HIS D 524 GLN D 552 GLN D 562 ASN D 598 GLN D 599 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 6618 Z= 0.355 Angle : 0.575 5.233 8987 Z= 0.300 Chirality : 0.046 0.211 946 Planarity : 0.004 0.041 1160 Dihedral : 3.976 20.672 885 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 780 helix: 0.71 (0.26), residues: 394 sheet: -0.28 (0.68), residues: 41 loop : -1.53 (0.30), residues: 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 0.735 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 172 average time/residue: 1.2566 time to fit residues: 226.2454 Evaluate side-chains 162 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 6 residues processed: 7 average time/residue: 0.3260 time to fit residues: 3.7052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 48 optimal weight: 0.0370 chunk 19 optimal weight: 0.0010 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 56 optimal weight: 0.0980 chunk 53 optimal weight: 0.0570 overall best weight: 0.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN D 220 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 6618 Z= 0.141 Angle : 0.489 10.439 8987 Z= 0.246 Chirality : 0.040 0.144 946 Planarity : 0.004 0.052 1160 Dihedral : 3.806 22.680 885 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 4.09 % 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 (0.30), residues: 780 helix: 1.20 (0.27), residues: 394 sheet: -0.07 (0.68), residues: 43 loop : -1.26 (0.31), residues: 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 0.770 Fit side-chains outliers start: 28 outliers final: 13 residues processed: 157 average time/residue: 1.2549 time to fit residues: 206.4805 Evaluate side-chains 160 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 6 average time/residue: 0.6434 time to fit residues: 5.1286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.0370 chunk 42 optimal weight: 0.3980 overall best weight: 0.3058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 220 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 578 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 6618 Z= 0.231 Angle : 0.514 6.661 8987 Z= 0.263 Chirality : 0.041 0.137 946 Planarity : 0.004 0.051 1160 Dihedral : 3.981 22.753 885 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer Outliers : 3.80 % 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: 0.28 (0.29), residues: 780 helix: 1.40 (0.27), residues: 383 sheet: 0.09 (0.75), residues: 43 loop : -1.19 (0.30), residues: 354 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 0.675 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 157 average time/residue: 1.2735 time to fit residues: 209.1987 Evaluate side-chains 163 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 0.738 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 7 residues processed: 7 average time/residue: 0.5503 time to fit residues: 5.2724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.0980 chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.0270 chunk 64 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.0470 chunk 14 optimal weight: 0.9990 overall best weight: 0.1336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 101 GLN D 220 ASN ** D 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 GLN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 6618 Z= 0.145 Angle : 0.478 7.280 8987 Z= 0.240 Chirality : 0.039 0.136 946 Planarity : 0.004 0.048 1160 Dihedral : 3.837 21.399 885 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 3.07 % 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: 0.58 (0.30), residues: 780 helix: 1.65 (0.27), residues: 383 sheet: 0.17 (0.72), residues: 43 loop : -1.03 (0.31), residues: 354 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 0.779 Fit side-chains outliers start: 21 outliers final: 12 residues processed: 162 average time/residue: 1.3047 time to fit residues: 222.0176 Evaluate side-chains 158 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 146 time to evaluate : 0.763 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.1702 time to fit residues: 1.9577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 62 optimal weight: 0.3980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 0.0870 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 GLN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 368 ASN D 578 ASN D 598 GLN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6618 Z= 0.223 Angle : 0.511 7.667 8987 Z= 0.257 Chirality : 0.041 0.132 946 Planarity : 0.004 0.046 1160 Dihedral : 3.960 20.797 885 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.30), residues: 780 helix: 1.54 (0.27), residues: 384 sheet: 0.28 (0.75), residues: 43 loop : -1.02 (0.31), residues: 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 153 time to evaluate : 0.751 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 165 average time/residue: 1.2193 time to fit residues: 211.0833 Evaluate side-chains 156 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.666 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 4 average time/residue: 0.5152 time to fit residues: 3.1845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.0870 chunk 63 optimal weight: 0.6980 chunk 75 optimal weight: 0.0050 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.0870 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 44 optimal weight: 0.0570 chunk 22 optimal weight: 0.0970 overall best weight: 0.0666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 101 GLN D 220 ASN D 578 ASN D 598 GLN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 6618 Z= 0.131 Angle : 0.501 11.695 8987 Z= 0.243 Chirality : 0.038 0.130 946 Planarity : 0.004 0.044 1160 Dihedral : 3.792 23.460 885 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 2.04 % 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: 0.88 (0.30), residues: 780 helix: 1.82 (0.28), residues: 384 sheet: 0.37 (0.72), residues: 43 loop : -0.79 (0.32), residues: 353 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 150 time to evaluate : 0.768 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 160 average time/residue: 1.2876 time to fit residues: 215.8908 Evaluate side-chains 152 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 0.736 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.2319 time to fit residues: 1.5564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 101 GLN D 102 GLN D 220 ASN D 368 ASN D 374 HIS D 531 GLN D 578 ASN D 598 GLN A 417 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 6618 Z= 0.415 Angle : 0.593 9.364 8987 Z= 0.300 Chirality : 0.045 0.158 946 Planarity : 0.005 0.047 1160 Dihedral : 4.268 24.203 885 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.29), residues: 780 helix: 1.21 (0.26), residues: 390 sheet: 0.19 (0.76), residues: 44 loop : -1.01 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.764 Fit side-chains outliers start: 18 outliers final: 13 residues processed: 162 average time/residue: 1.2937 time to fit residues: 219.8438 Evaluate side-chains 162 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.8002 time to fit residues: 3.6638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 63 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 0.1980 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN D 101 GLN D 220 ASN D 493 HIS D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6618 Z= 0.170 Angle : 0.530 10.039 8987 Z= 0.263 Chirality : 0.040 0.131 946 Planarity : 0.004 0.045 1160 Dihedral : 4.024 23.210 885 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.04 % 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: 0.60 (0.30), residues: 780 helix: 1.50 (0.27), residues: 388 sheet: 0.39 (0.75), residues: 43 loop : -0.88 (0.31), residues: 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 155 time to evaluate : 0.657 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 1.2702 time to fit residues: 218.4964 Evaluate side-chains 157 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.1114 time to fit residues: 1.3421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0060 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 49 optimal weight: 0.0980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.3980 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 31 ASN ** D 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN D 330 ASN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 6618 Z= 0.234 Angle : 0.538 9.524 8987 Z= 0.268 Chirality : 0.041 0.131 946 Planarity : 0.004 0.049 1160 Dihedral : 4.095 23.050 885 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.34 % 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: 0.48 (0.30), residues: 780 helix: 1.40 (0.27), residues: 390 sheet: 0.41 (0.75), residues: 43 loop : -0.94 (0.31), residues: 347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.714 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 158 average time/residue: 1.2697 time to fit residues: 211.1032 Evaluate side-chains 154 residues out of total 685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 0.777 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 11 residues processed: 0 time to fit residues: 1.0854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 63 optimal weight: 0.0170 chunk 7 optimal weight: 0.3980 chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 70 optimal weight: 0.4980 chunk 41 optimal weight: 0.3980 overall best weight: 0.2018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN D 220 ASN D 368 ASN D 578 ASN D 598 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.135010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.124717 restraints weight = 9173.606| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.68 r_work: 0.3644 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 6618 Z= 0.186 Angle : 0.530 9.595 8987 Z= 0.263 Chirality : 0.040 0.129 946 Planarity : 0.004 0.048 1160 Dihedral : 4.025 22.396 885 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer Outliers : 1.90 % 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: 0.62 (0.30), residues: 780 helix: 1.50 (0.27), residues: 390 sheet: 0.38 (0.74), residues: 43 loop : -0.85 (0.32), residues: 347 =============================================================================== Job complete usr+sys time: 4084.53 seconds wall clock time: 73 minutes 11.19 seconds (4391.19 seconds total)