Starting phenix.real_space_refine (version: 1.20rc2) on Tue Nov 2 01:46:01 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pmw_13542/11_2021/7pmw_13542.pdb" } resolution = 4.1 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 507": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc2-4405/modules/chem_data/mon_lib" Total number of atoms: 10153 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 10120 Classifications: {'peptide': 641} Link IDs: {'PTRANS': 29, 'TRANS': 611} Chain breaks: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.50 Number of scatterers: 10153 At special positions: 0 Unit cell: (82.41, 91.12, 120.6, 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) S 32 16.00 O 894 8.00 N 806 7.00 C 3298 6.00 H 5123 1.00 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 Amimo acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.55 Conformation dependent library (CDL) restraints added in 844.2 milliseconds 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1202 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 5 sheets defined 60.8% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 42 removed outlier: 4.233A pdb=" N ILE A 16 " --> pdb=" O TYR A 12 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 removed outlier: 3.622A pdb=" N TYR A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 77 removed outlier: 3.905A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 108 removed outlier: 3.630A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 149 removed outlier: 3.784A pdb=" N SER A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.681A pdb=" N SER A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 181 removed outlier: 3.718A pdb=" N ASN A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER A 174 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 219 Proline residue: A 205 - end of helix removed outlier: 3.712A pdb=" N MET A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 231 through 249 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.661A pdb=" N ALA A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 287 removed outlier: 3.775A pdb=" N LEU A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 298 removed outlier: 4.126A pdb=" N TRP A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 4.206A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TRP A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N THR A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 326 through 343 removed outlier: 4.034A pdb=" N ALA A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.557A pdb=" N ASP A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 356 through 383 removed outlier: 3.745A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 383 " --> pdb=" O GLN A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 removed outlier: 3.664A pdb=" N GLU A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 610 removed outlier: 4.698A pdb=" N GLN A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 637 removed outlier: 3.768A pdb=" N LEU A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 626 " --> pdb=" O TRP A 622 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA A 637 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 removed outlier: 4.067A pdb=" N ALA A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 5.626A pdb=" N TYR A 672 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.199A pdb=" N ALA A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423 removed outlier: 6.845A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.614A pdb=" N GLY A 487 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N TYR A 556 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG A 489 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N VAL A 558 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA A 553 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 505 through 510 removed outlier: 6.303A pdb=" N ILE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 265 hydrogen bonds defined for protein. 747 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 8.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5113 1.03 - 1.23: 12 1.23 - 1.42: 2135 1.42 - 1.61: 2957 1.61 - 1.81: 54 Bond restraints: 10271 Sorted by residual: bond pdb=" N ASN A 329 " pdb=" CA ASN A 329 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.23e-02 6.61e+03 7.80e+00 bond pdb=" N ASN A 329 " pdb=" H ASN A 329 " ideal model delta sigma weight residual 0.860 0.914 -0.054 2.00e-02 2.50e+03 7.25e+00 bond pdb=" C ASN A 329 " pdb=" O ASN A 329 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.19e-02 7.06e+03 4.39e+00 bond pdb=" C ASN A 329 " pdb=" N ALA A 330 " ideal model delta sigma weight residual 1.335 1.310 0.025 1.36e-02 5.41e+03 3.25e+00 bond pdb=" ND2 ASN A 329 " pdb="HD22 ASN A 329 " ideal model delta sigma weight residual 0.860 0.885 -0.025 2.00e-02 2.50e+03 1.53e+00 ... (remaining 10266 not shown) Histogram of bond angle deviations from ideal: 73.89 - 85.92: 6 85.92 - 97.94: 0 97.94 - 109.97: 8830 109.97 - 122.00: 8196 122.00 - 134.03: 1560 Bond angle restraints: 18592 Sorted by residual: angle pdb=" C LEU A 51 " pdb=" CA LEU A 51 " pdb=" HA LEU A 51 " ideal model delta sigma weight residual 109.00 73.89 35.11 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C GLN A 609 " pdb=" CA GLN A 609 " pdb=" HA GLN A 609 " ideal model delta sigma weight residual 109.00 74.26 34.74 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N GLN A 609 " pdb=" CA GLN A 609 " pdb=" HA GLN A 609 " ideal model delta sigma weight residual 110.00 75.29 34.71 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU A 51 " pdb=" CA LEU A 51 " pdb=" HA LEU A 51 " ideal model delta sigma weight residual 110.00 75.86 34.14 3.00e+00 1.11e-01 1.30e+02 angle pdb=" CB LEU A 51 " pdb=" CA LEU A 51 " pdb=" HA LEU A 51 " ideal model delta sigma weight residual 109.00 75.27 33.73 3.00e+00 1.11e-01 1.26e+02 ... (remaining 18587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3957 17.96 - 35.92: 148 35.92 - 53.88: 16 53.88 - 71.84: 7 71.84 - 89.80: 5 Dihedral angle restraints: 4133 sinusoidal: 1866 harmonic: 2267 Sorted by residual: dihedral pdb=" C LEU A 51 " pdb=" N LEU A 51 " pdb=" CA LEU A 51 " pdb=" CB LEU A 51 " ideal model delta harmonic sigma weight residual -122.60 -131.99 9.39 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" C GLN A 609 " pdb=" N GLN A 609 " pdb=" CA GLN A 609 " pdb=" CB GLN A 609 " ideal model delta harmonic sigma weight residual -122.60 -131.75 9.15 0 2.50e+00 1.60e-01 1.34e+01 dihedral pdb=" C ASN A 329 " pdb=" N ASN A 329 " pdb=" CA ASN A 329 " pdb=" CB ASN A 329 " ideal model delta harmonic sigma weight residual -122.60 -113.57 -9.03 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 4130 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 758 0.078 - 0.156: 49 0.156 - 0.234: 0 0.234 - 0.311: 0 0.311 - 0.389: 2 Chirality restraints: 809 Sorted by residual: chirality pdb=" CA GLN A 609 " pdb=" N GLN A 609 " pdb=" C GLN A 609 " pdb=" CB GLN A 609 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA LEU A 51 " pdb=" N LEU A 51 " pdb=" C LEU A 51 " pdb=" CB LEU A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 806 not shown) Planarity restraints: 1482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " 0.107 2.00e-02 2.50e+03 1.13e-01 1.93e+02 pdb=" CG ASN A 329 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " -0.101 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 329 " 0.168 2.00e-02 2.50e+03 pdb="HD22 ASN A 329 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 535 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.28e+00 pdb=" N PRO A 536 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 585 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO A 586 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " -0.014 5.00e-02 4.00e+02 ... (remaining 1479 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 70 1.95 - 2.61: 11824 2.61 - 3.28: 30968 3.28 - 3.94: 36170 3.94 - 4.60: 57202 Nonbonded interactions: 136234 Sorted by model distance: nonbonded pdb="HD22 ASN A 171 " pdb="HD13 ILE A 333 " model vdw 1.291 2.270 nonbonded pdb="HD21 ASN A 171 " pdb="HG21 ILE A 333 " model vdw 1.293 2.270 nonbonded pdb=" HB3 HIS A 57 " pdb="HD21 ASN A 630 " model vdw 1.554 2.270 nonbonded pdb=" H ARG A 258 " pdb=" OD2 ASP A 263 " model vdw 1.613 1.850 nonbonded pdb=" O GLY A 419 " pdb=" HG SER A 422 " model vdw 1.615 1.850 ... (remaining 136229 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 S 32 5.16 5 C 3298 2.51 5 N 806 2.21 5 O 894 1.98 5 H 5123 0.53 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 group one per residue Write .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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.250 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.080 Process input model: 34.320 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.002 0.034 5148 Z= 0.124 Angle : 0.467 9.658 6989 Z= 0.259 Chirality : 0.043 0.389 809 Planarity : 0.003 0.028 873 Dihedral : 9.249 54.339 1835 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.17 % 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: 0.56 (0.35), residues: 633 helix: 0.74 (0.31), residues: 297 sheet: 1.33 (0.64), residues: 71 loop : -0.19 (0.41), residues: 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 142 average time/residue: 0.3456 time to fit residues: 63.2609 Evaluate side-chains 95 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.887 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5630 time to fit residues: 2.2257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 379 GLN ** A 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 5148 Z= 0.176 Angle : 0.540 4.956 6989 Z= 0.295 Chirality : 0.045 0.400 809 Planarity : 0.004 0.037 873 Dihedral : 4.282 14.922 680 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.34), residues: 633 helix: 0.94 (0.28), residues: 314 sheet: 0.96 (0.62), residues: 73 loop : -0.08 (0.44), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3029 time to fit residues: 43.9764 Evaluate side-chains 86 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.856 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 GLN A 379 GLN A 609 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5148 Z= 0.197 Angle : 0.513 5.990 6989 Z= 0.280 Chirality : 0.044 0.393 809 Planarity : 0.004 0.052 873 Dihedral : 4.366 15.585 680 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.34), residues: 633 helix: 0.85 (0.28), residues: 316 sheet: 0.56 (0.60), residues: 73 loop : -0.24 (0.43), residues: 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.3041 time to fit residues: 39.6868 Evaluate side-chains 84 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5148 Z= 0.176 Angle : 0.498 5.274 6989 Z= 0.267 Chirality : 0.044 0.394 809 Planarity : 0.004 0.042 873 Dihedral : 4.310 15.241 680 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.34), residues: 633 helix: 0.99 (0.28), residues: 318 sheet: 0.41 (0.61), residues: 73 loop : -0.09 (0.44), residues: 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 97 average time/residue: 0.2877 time to fit residues: 38.1394 Evaluate side-chains 79 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 5148 Z= 0.259 Angle : 0.534 5.159 6989 Z= 0.292 Chirality : 0.044 0.396 809 Planarity : 0.004 0.038 873 Dihedral : 4.578 16.519 680 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.34), residues: 633 helix: 0.76 (0.28), residues: 320 sheet: 0.29 (0.63), residues: 67 loop : -0.24 (0.44), residues: 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.3005 time to fit residues: 39.1900 Evaluate side-chains 82 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.835 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 9.9990 chunk 15 optimal weight: 0.0980 chunk 61 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.0870 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 379 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 5148 Z= 0.139 Angle : 0.479 5.392 6989 Z= 0.250 Chirality : 0.044 0.389 809 Planarity : 0.003 0.034 873 Dihedral : 4.204 14.378 680 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.35), residues: 633 helix: 1.20 (0.29), residues: 320 sheet: 0.39 (0.63), residues: 67 loop : -0.14 (0.44), residues: 246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2971 time to fit residues: 36.4901 Evaluate side-chains 79 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 379 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5148 Z= 0.194 Angle : 0.498 5.377 6989 Z= 0.265 Chirality : 0.043 0.394 809 Planarity : 0.004 0.039 873 Dihedral : 4.265 14.673 680 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 633 helix: 1.21 (0.29), residues: 318 sheet: 0.34 (0.63), residues: 67 loop : -0.20 (0.43), residues: 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3013 time to fit residues: 36.1831 Evaluate side-chains 79 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.812 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 0.0670 chunk 5 optimal weight: 0.3980 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 overall best weight: 2.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5148 Z= 0.196 Angle : 0.504 6.496 6989 Z= 0.267 Chirality : 0.044 0.394 809 Planarity : 0.004 0.040 873 Dihedral : 4.285 14.927 680 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.35), residues: 633 helix: 1.23 (0.29), residues: 318 sheet: 0.37 (0.64), residues: 67 loop : -0.17 (0.43), residues: 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2964 time to fit residues: 34.7984 Evaluate side-chains 73 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.818 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 0.0870 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 60 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 5148 Z= 0.143 Angle : 0.484 5.478 6989 Z= 0.253 Chirality : 0.043 0.389 809 Planarity : 0.004 0.041 873 Dihedral : 4.151 15.340 680 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.35), residues: 633 helix: 1.36 (0.29), residues: 318 sheet: 0.46 (0.64), residues: 67 loop : -0.13 (0.43), residues: 248 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3034 time to fit residues: 35.1765 Evaluate side-chains 78 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.0980 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 46 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 5148 Z= 0.186 Angle : 0.504 5.556 6989 Z= 0.267 Chirality : 0.043 0.393 809 Planarity : 0.004 0.043 873 Dihedral : 4.195 14.372 680 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.35), residues: 633 helix: 1.32 (0.29), residues: 318 sheet: 0.45 (0.64), residues: 67 loop : -0.15 (0.43), residues: 248 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1266 Ramachandran restraints generated. 633 Oldfield, 0 Emsley, 633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2836 time to fit residues: 33.1888 Evaluate side-chains 73 residues out of total 549 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.757 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.121226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.099809 restraints weight = 46017.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.103048 restraints weight = 26932.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105315 restraints weight = 18945.710| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5148 Z= 0.225 Angle : 0.519 5.600 6989 Z= 0.278 Chirality : 0.044 0.396 809 Planarity : 0.004 0.044 873 Dihedral : 4.347 16.301 680 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.35), residues: 633 helix: 1.16 (0.29), residues: 320 sheet: 0.39 (0.63), residues: 67 loop : -0.15 (0.44), residues: 246 =============================================================================== Job complete usr+sys time: 2637.12 seconds wall clock time: 47 minutes 22.65 seconds (2842.65 seconds total)