Starting phenix.real_space_refine (version: dev) on Mon Dec 12 09:42:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/12_2022/7mo8_23920_updated.pdb" } resolution = 4.5 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= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9877 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4937 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 38, 'TRANS': 595} Chain breaks: 6 Unresolved non-hydrogen bonds: 180 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 4843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4843 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 583} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 97 Unusual residues: {'IDS': 3, 'SGN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.06, per 1000 atoms: 0.61 Number of scatterers: 9877 At special positions: 0 Unit cell: (114.48, 122.04, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 1863 8.00 N 1711 7.00 C 6207 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 283 " distance=2.02 Simple disulfide: pdb=" SG CYS A 305 " - pdb=" SG CYS A 383 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 365 " distance=2.02 Simple disulfide: pdb=" SG CYS A 354 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 412 " - pdb=" SG CYS A 452 " distance=2.02 Simple disulfide: pdb=" SG CYS A 440 " - pdb=" SG CYS A 464 " distance=2.03 Simple disulfide: pdb=" SG CYS A 519 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 679 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 697 " distance=2.04 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 584 " distance=2.03 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 98 " - pdb=" SG CYS B 160 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 363 " distance=2.02 Simple disulfide: pdb=" SG CYS B 385 " - pdb=" SG CYS B 397 " distance=2.04 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 538 " distance=2.03 Simple disulfide: pdb=" SG CYS B 526 " - pdb=" SG CYS B 561 " distance=2.04 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 545 " distance=2.03 Simple disulfide: pdb=" SG CYS B 541 " - pdb=" SG CYS B 551 " distance=2.02 Simple disulfide: pdb=" SG CYS B 610 " - pdb=" SG CYS B 624 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " IDS D 2 " - " SGN D 3 " " IDS D 4 " - " SGN D 5 " BETA1-4 " SGN D 1 " - " IDS D 2 " ~> Even though IDS is an alpha isomer, a beta linkage is required... " SGN D 3 " - " IDS D 4 " " SGN D 5 " - " IDS D 6 " Time building additional restraints: 4.56 Conformation dependent library (CDL) restraints added in 1.4 seconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 20 sheets defined 8.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 639 through 645 Processing helix chain 'A' and resid 709 through 711 No H-bonds generated for 'chain 'A' and resid 709 through 711' Processing helix chain 'A' and resid 713 through 720 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 327 through 333 Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 387 through 390 No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 495 through 497 No H-bonds generated for 'chain 'B' and resid 495 through 497' Processing helix chain 'B' and resid 526 through 531 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 614 through 616 No H-bonds generated for 'chain 'B' and resid 614 through 616' Processing sheet with id= A, first strand: chain 'A' and resid 49 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 61 through 63 removed outlier: 3.938A pdb=" N GLN A 95 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP A 90 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 270 through 272 Processing sheet with id= D, first strand: chain 'A' and resid 451 through 453 Processing sheet with id= E, first strand: chain 'A' and resid 508 through 513 removed outlier: 4.213A pdb=" N CYS A 519 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR A 513 " --> pdb=" O HIS A 517 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N HIS A 517 " --> pdb=" O TYR A 513 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N GLY A 520 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA A 532 " --> pdb=" O GLY A 520 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 546 through 548 Processing sheet with id= G, first strand: chain 'A' and resid 612 through 616 Processing sheet with id= H, first strand: chain 'A' and resid 656 through 659 Processing sheet with id= I, first strand: chain 'A' and resid 676 through 680 removed outlier: 5.447A pdb=" N CYS A 679 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 687 " --> pdb=" O CYS A 679 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 44 through 47 Processing sheet with id= K, first strand: chain 'B' and resid 61 through 66 removed outlier: 3.923A pdb=" N ALA B 82 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN B 74 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 80 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 89 through 91 Processing sheet with id= M, first strand: chain 'B' and resid 120 through 123 Processing sheet with id= N, first strand: chain 'B' and resid 181 through 189 removed outlier: 4.509A pdb=" N ILE B 193 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 292 through 295 removed outlier: 3.528A pdb=" N GLN B 265 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL B 264 " --> pdb=" O TYR B 249 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR B 249 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 424 through 427 removed outlier: 4.219A pdb=" N CYS B 298 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 312 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 360 through 366 removed outlier: 3.521A pdb=" N ALA B 319 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA B 347 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU B 317 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 444 through 447 removed outlier: 4.641A pdb=" N THR B 451 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 621 through 624 removed outlier: 6.040A pdb=" N TRP B 586 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ILE B 565 " --> pdb=" O TRP B 586 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 602 through 604 182 hydrogen bonds defined for protein. 465 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: 3.42 Time building geometry restraints manager: 4.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3219 1.34 - 1.46: 2479 1.46 - 1.59: 4317 1.59 - 1.71: 1 1.71 - 1.83: 112 Bond restraints: 10128 Sorted by residual: bond pdb=" O6 SGN D 1 " pdb=" S2 SGN D 1 " ideal model delta sigma weight residual 1.660 1.510 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" N SGN D 3 " pdb=" S1 SGN D 3 " ideal model delta sigma weight residual 1.713 1.584 0.129 2.00e-02 2.50e+03 4.18e+01 bond pdb=" O6 SGN D 3 " pdb=" S2 SGN D 3 " ideal model delta sigma weight residual 1.660 1.536 0.124 2.00e-02 2.50e+03 3.87e+01 bond pdb=" O2 IDS D 6 " pdb=" S IDS D 6 " ideal model delta sigma weight residual 1.651 1.528 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O2 IDS D 2 " pdb=" S IDS D 2 " ideal model delta sigma weight residual 1.651 1.543 0.108 2.00e-02 2.50e+03 2.90e+01 ... (remaining 10123 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.88: 219 104.88 - 112.18: 5134 112.18 - 119.48: 3150 119.48 - 126.78: 5088 126.78 - 134.09: 170 Bond angle restraints: 13761 Sorted by residual: angle pdb=" N THR B 86 " pdb=" CA THR B 86 " pdb=" C THR B 86 " ideal model delta sigma weight residual 110.65 104.83 5.82 1.26e+00 6.30e-01 2.14e+01 angle pdb=" C ARG A 441 " pdb=" N ASN A 442 " pdb=" CA ASN A 442 " ideal model delta sigma weight residual 122.21 109.29 12.92 2.87e+00 1.21e-01 2.03e+01 angle pdb=" N ARG B 592 " pdb=" CA ARG B 592 " pdb=" C ARG B 592 " ideal model delta sigma weight residual 110.42 104.34 6.08 1.55e+00 4.16e-01 1.54e+01 angle pdb=" C6 SGN D 1 " pdb=" C5 SGN D 1 " pdb=" O5 SGN D 1 " ideal model delta sigma weight residual 108.92 97.58 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C2 IDS D 2 " pdb=" O2 IDS D 2 " pdb=" S IDS D 2 " ideal model delta sigma weight residual 115.98 127.31 -11.33 3.00e+00 1.11e-01 1.43e+01 ... (remaining 13756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5234 17.97 - 35.93: 626 35.93 - 53.90: 145 53.90 - 71.87: 36 71.87 - 89.84: 11 Dihedral angle restraints: 6052 sinusoidal: 2435 harmonic: 3617 Sorted by residual: dihedral pdb=" CB CYS A 305 " pdb=" SG CYS A 305 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual 93.00 177.14 -84.14 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS B 541 " pdb=" SG CYS B 541 " pdb=" SG CYS B 551 " pdb=" CB CYS B 551 " ideal model delta sinusoidal sigma weight residual 93.00 172.23 -79.23 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS A 70 " pdb=" SG CYS A 70 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual -86.00 -161.25 75.25 1 1.00e+01 1.00e-02 7.16e+01 ... (remaining 6049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1002 0.043 - 0.085: 362 0.085 - 0.128: 115 0.128 - 0.170: 13 0.170 - 0.213: 5 Chirality restraints: 1497 Sorted by residual: chirality pdb=" C1 IDS D 2 " pdb=" O4 SGN D 1 " pdb=" C2 IDS D 2 " pdb=" O5 IDS D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.35e+01 chirality pdb=" C1 SGN D 5 " pdb=" O4 IDS D 4 " pdb=" C2 SGN D 5 " pdb=" O5 SGN D 5 " both_signs ideal model delta sigma weight residual False 2.40 2.30 0.10 2.00e-02 2.50e+03 2.68e+01 chirality pdb=" C1 IDS D 4 " pdb=" O4 SGN D 3 " pdb=" C2 IDS D 4 " pdb=" O5 IDS D 4 " both_signs ideal model delta sigma weight residual False -2.40 -2.49 0.09 2.00e-02 2.50e+03 1.83e+01 ... (remaining 1494 not shown) Planarity restraints: 1774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 459 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 460 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 573 " -0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 574 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 574 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 574 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 156 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.05e+00 pdb=" N PRO A 157 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.028 5.00e-02 4.00e+02 ... (remaining 1771 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 266 2.64 - 3.20: 10123 3.20 - 3.77: 16393 3.77 - 4.33: 22466 4.33 - 4.90: 34274 Nonbonded interactions: 83522 Sorted by model distance: nonbonded pdb=" OG SER A 360 " pdb=" O SER A 362 " model vdw 2.070 2.440 nonbonded pdb=" O CYS B 541 " pdb=" ND1 HIS B 542 " model vdw 2.100 2.520 nonbonded pdb=" OG1 THR A 454 " pdb=" O ILE A 459 " model vdw 2.107 2.440 nonbonded pdb=" O LYS B 248 " pdb=" OG1 THR B 263 " model vdw 2.115 2.440 nonbonded pdb=" NZ LYS B 567 " pdb=" O VAL B 568 " model vdw 2.116 2.520 ... (remaining 83517 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 6207 2.51 5 N 1711 2.21 5 O 1863 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 group one per residue 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: 1.410 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: 5.500 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.080 Process input model: 30.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 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 : 0.008 0.150 10128 Z= 0.504 Angle : 1.001 12.917 13761 Z= 0.545 Chirality : 0.048 0.213 1497 Planarity : 0.005 0.066 1774 Dihedral : 16.573 89.836 3631 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 31.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.95 (0.23), residues: 1228 helix: -1.92 (0.50), residues: 87 sheet: -0.86 (0.33), residues: 256 loop : -1.44 (0.21), residues: 885 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2704 time to fit residues: 35.4825 Evaluate side-chains 49 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.232 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.0980 chunk 63 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 0.0970 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 681 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 202 ASN B 318 GLN ** B 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 10128 Z= 0.197 Angle : 0.654 9.937 13761 Z= 0.330 Chirality : 0.046 0.300 1497 Planarity : 0.005 0.055 1774 Dihedral : 6.604 53.503 1355 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.72 (0.24), residues: 1228 helix: -1.85 (0.47), residues: 88 sheet: -0.66 (0.33), residues: 252 loop : -1.28 (0.21), residues: 888 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 75 average time/residue: 0.2089 time to fit residues: 23.3548 Evaluate side-chains 50 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 8.9990 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 112 optimal weight: 0.0770 chunk 121 optimal weight: 0.0980 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 10128 Z= 0.237 Angle : 0.649 8.801 13761 Z= 0.329 Chirality : 0.045 0.250 1497 Planarity : 0.005 0.079 1774 Dihedral : 6.405 53.817 1355 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.71 (0.24), residues: 1228 helix: -2.08 (0.45), residues: 91 sheet: -0.64 (0.33), residues: 254 loop : -1.24 (0.21), residues: 883 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 74 average time/residue: 0.2166 time to fit residues: 24.0538 Evaluate side-chains 47 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 129 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10128 Z= 0.289 Angle : 0.666 8.016 13761 Z= 0.340 Chirality : 0.045 0.225 1497 Planarity : 0.006 0.138 1774 Dihedral : 6.477 53.613 1355 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 24.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.75 (0.24), residues: 1228 helix: -2.11 (0.44), residues: 89 sheet: -0.81 (0.32), residues: 266 loop : -1.22 (0.21), residues: 873 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 1.304 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.1993 time to fit residues: 19.2927 Evaluate side-chains 44 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 114 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10128 Z= 0.297 Angle : 0.670 8.061 13761 Z= 0.346 Chirality : 0.045 0.202 1497 Planarity : 0.005 0.065 1774 Dihedral : 6.489 53.848 1355 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.80 (0.24), residues: 1228 helix: -2.10 (0.44), residues: 88 sheet: -0.83 (0.32), residues: 266 loop : -1.27 (0.21), residues: 874 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.109 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.2022 time to fit residues: 17.8746 Evaluate side-chains 42 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 119 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10128 Z= 0.186 Angle : 0.596 10.033 13761 Z= 0.304 Chirality : 0.044 0.171 1497 Planarity : 0.004 0.049 1774 Dihedral : 6.071 51.983 1355 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.58 (0.24), residues: 1228 helix: -1.68 (0.48), residues: 87 sheet: -0.79 (0.31), residues: 281 loop : -1.11 (0.22), residues: 860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.169 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1834 time to fit residues: 17.9364 Evaluate side-chains 46 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 10128 Z= 0.204 Angle : 0.594 8.487 13761 Z= 0.305 Chirality : 0.044 0.185 1497 Planarity : 0.004 0.050 1774 Dihedral : 5.954 52.458 1355 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.52 (0.24), residues: 1228 helix: -1.65 (0.48), residues: 89 sheet: -0.78 (0.31), residues: 279 loop : -1.04 (0.22), residues: 860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.261 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1933 time to fit residues: 18.3108 Evaluate side-chains 47 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 0.0170 chunk 11 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 10128 Z= 0.227 Angle : 0.606 8.632 13761 Z= 0.309 Chirality : 0.043 0.162 1497 Planarity : 0.004 0.048 1774 Dihedral : 5.994 52.926 1355 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.49 (0.24), residues: 1228 helix: -1.54 (0.50), residues: 89 sheet: -0.78 (0.30), residues: 279 loop : -1.02 (0.22), residues: 860 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2209 time to fit residues: 20.4926 Evaluate side-chains 46 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.211 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 67 optimal weight: 0.0670 chunk 48 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 100 optimal weight: 9.9990 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 overall best weight: 2.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 10128 Z= 0.213 Angle : 0.592 8.519 13761 Z= 0.303 Chirality : 0.043 0.160 1497 Planarity : 0.004 0.065 1774 Dihedral : 5.944 52.516 1355 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.45 (0.24), residues: 1228 helix: -1.45 (0.51), residues: 88 sheet: -0.77 (0.30), residues: 279 loop : -0.99 (0.22), residues: 861 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.2013 time to fit residues: 19.3545 Evaluate side-chains 45 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 123 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 10128 Z= 0.315 Angle : 0.678 8.649 13761 Z= 0.350 Chirality : 0.044 0.168 1497 Planarity : 0.005 0.051 1774 Dihedral : 6.409 54.766 1355 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.66 (0.24), residues: 1228 helix: -1.65 (0.49), residues: 88 sheet: -0.86 (0.31), residues: 265 loop : -1.16 (0.21), residues: 875 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 0.2082 time to fit residues: 18.7642 Evaluate side-chains 44 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.037942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.032612 restraints weight = 118277.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.033389 restraints weight = 80865.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.033933 restraints weight = 59636.324| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10128 Z= 0.194 Angle : 0.592 8.546 13761 Z= 0.300 Chirality : 0.043 0.159 1497 Planarity : 0.004 0.050 1774 Dihedral : 5.981 53.080 1355 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: -1.49 (0.24), residues: 1228 helix: -1.47 (0.50), residues: 88 sheet: -0.80 (0.31), residues: 268 loop : -1.03 (0.22), residues: 872 =============================================================================== Job complete usr+sys time: 1636.37 seconds wall clock time: 31 minutes 12.27 seconds (1872.27 seconds total)