Starting phenix.real_space_refine on Wed Feb 14 17:44:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/02_2024/7mo8_23920_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/02_2024/7mo8_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_23920/02_2024/7mo8_23920.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/02_2024/7mo8_23920.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/02_2024/7mo8_23920_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mo8_23920/02_2024/7mo8_23920_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 28 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.58, per 1000 atoms: 0.56 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: 4.58 Conformation dependent library (CDL) restraints added in 1.7 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: 2.08 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: 3.02 Time building geometry restraints manager: 4.87 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 1.646 1.528 0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" O2 IDS D 2 " pdb=" S IDS D 2 " ideal model delta sigma weight residual 1.646 1.543 0.103 2.00e-02 2.50e+03 2.64e+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=" C1 IDS D 4 " pdb=" C2 IDS D 4 " pdb=" O2 IDS D 4 " ideal model delta sigma weight residual 105.22 119.24 -14.02 3.00e+00 1.11e-01 2.19e+01 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=" O1S IDS D 2 " pdb=" S IDS D 2 " pdb=" O2 IDS D 2 " ideal model delta sigma weight residual 101.14 113.20 -12.06 3.00e+00 1.11e-01 1.62e+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 ... (remaining 13756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.99: 5660 25.99 - 51.99: 429 51.99 - 77.98: 45 77.98 - 103.97: 23 103.97 - 129.96: 18 Dihedral angle restraints: 6175 sinusoidal: 2558 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 6172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1054 0.047 - 0.093: 347 0.093 - 0.140: 83 0.140 - 0.187: 11 0.187 - 0.234: 2 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 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: 0.970 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: 4.680 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 30.070 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 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= 0.512 Angle : 1.016 14.024 13761 Z= 0.549 Chirality : 0.048 0.234 1497 Planarity : 0.005 0.066 1774 Dihedral : 19.618 129.964 3754 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 31.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 415 HIS 0.010 0.002 HIS B 275 PHE 0.029 0.003 PHE B 192 TYR 0.020 0.003 TYR A 635 ARG 0.013 0.002 ARG B 218 *********************** 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 : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 TYR cc_start: 0.8480 (m-80) cc_final: 0.8204 (m-10) REVERT: B 27 LYS cc_start: 0.8013 (mppt) cc_final: 0.7611 (tptt) REVERT: B 276 THR cc_start: 0.8182 (m) cc_final: 0.7888 (p) REVERT: B 278 ILE cc_start: 0.9422 (tt) cc_final: 0.9149 (pt) REVERT: B 619 MET cc_start: 0.8031 (pmm) cc_final: 0.7607 (tmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2768 time to fit residues: 36.1329 Evaluate side-chains 50 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 601 ASN A 681 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 GLN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10128 Z= 0.205 Angle : 0.667 11.559 13761 Z= 0.332 Chirality : 0.047 0.348 1497 Planarity : 0.005 0.055 1774 Dihedral : 15.077 115.935 1478 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.47 % Allowed : 12.31 % Favored : 87.22 % 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: -1.77 (0.24), residues: 1228 helix: -1.88 (0.47), residues: 89 sheet: -0.69 (0.33), residues: 254 loop : -1.31 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 415 HIS 0.006 0.001 HIS B 275 PHE 0.012 0.002 PHE B 596 TYR 0.015 0.002 TYR A 176 ARG 0.004 0.001 ARG A 178 *********************** 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 76 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6424 (mmtt) cc_final: 0.6155 (mmtt) REVERT: A 508 MET cc_start: 0.9125 (mmm) cc_final: 0.8872 (mmp) REVERT: A 511 LEU cc_start: 0.8835 (tt) cc_final: 0.8319 (mt) REVERT: A 615 TYR cc_start: 0.8438 (m-80) cc_final: 0.8087 (m-10) REVERT: B 27 LYS cc_start: 0.7923 (mppt) cc_final: 0.7530 (tptt) REVERT: B 278 ILE cc_start: 0.9429 (tt) cc_final: 0.9181 (pt) REVERT: B 333 ILE cc_start: 0.8980 (pt) cc_final: 0.8673 (mm) REVERT: B 362 MET cc_start: 0.8325 (tmm) cc_final: 0.7708 (ttp) REVERT: B 463 MET cc_start: 0.6662 (mtm) cc_final: 0.6184 (pmm) outliers start: 5 outliers final: 1 residues processed: 76 average time/residue: 0.2054 time to fit residues: 23.3910 Evaluate side-chains 50 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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: 0.7980 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 76 optimal weight: 0.0670 chunk 31 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.3522 ------------------------------------------------------------------------------- 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 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 129 GLN ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 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: 0.7489 moved from start: 0.2390 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= 0.198 Angle : 0.627 8.778 13761 Z= 0.313 Chirality : 0.046 0.307 1497 Planarity : 0.004 0.051 1774 Dihedral : 14.519 111.901 1478 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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: -1.55 (0.24), residues: 1228 helix: -1.74 (0.49), residues: 84 sheet: -0.53 (0.33), residues: 251 loop : -1.16 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 428 HIS 0.016 0.001 HIS B 275 PHE 0.018 0.001 PHE B 192 TYR 0.021 0.001 TYR A 250 ARG 0.008 0.001 ARG B 304 *********************** 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 72 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6537 (mmtt) cc_final: 0.5947 (tppt) REVERT: A 508 MET cc_start: 0.9109 (mmm) cc_final: 0.8862 (mmp) REVERT: A 511 LEU cc_start: 0.8897 (tt) cc_final: 0.8411 (mt) REVERT: A 615 TYR cc_start: 0.8389 (m-80) cc_final: 0.8104 (m-80) REVERT: A 677 LEU cc_start: 0.8806 (tp) cc_final: 0.8287 (mp) REVERT: B 278 ILE cc_start: 0.9403 (tt) cc_final: 0.9132 (pt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2405 time to fit residues: 25.4137 Evaluate side-chains 48 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 10.0000 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 0.0870 chunk 75 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 overall best weight: 3.6564 ------------------------------------------------------------------------------- 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 343 ASN A 371 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS ** 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: 0.7547 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10128 Z= 0.283 Angle : 0.665 8.965 13761 Z= 0.336 Chirality : 0.046 0.297 1497 Planarity : 0.005 0.050 1774 Dihedral : 14.146 109.900 1478 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 22.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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: -1.61 (0.24), residues: 1228 helix: -1.67 (0.48), residues: 83 sheet: -0.66 (0.33), residues: 253 loop : -1.19 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 415 HIS 0.011 0.002 HIS B 275 PHE 0.018 0.002 PHE A 536 TYR 0.015 0.002 TYR A 544 ARG 0.011 0.001 ARG B 277 *********************** 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 56 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6464 (mmtt) cc_final: 0.6008 (tppt) REVERT: A 508 MET cc_start: 0.9134 (mmm) cc_final: 0.8916 (mmp) REVERT: A 511 LEU cc_start: 0.9066 (tt) cc_final: 0.8500 (mt) REVERT: A 615 TYR cc_start: 0.8378 (m-80) cc_final: 0.8094 (m-80) REVERT: A 686 MET cc_start: 0.8554 (mtm) cc_final: 0.8244 (mtm) REVERT: B 278 ILE cc_start: 0.9441 (tt) cc_final: 0.9199 (pt) REVERT: B 294 MET cc_start: 0.8642 (tpt) cc_final: 0.8195 (tpp) REVERT: B 463 MET cc_start: 0.6808 (mtm) cc_final: 0.6389 (pmm) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2083 time to fit residues: 17.8378 Evaluate side-chains 42 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 42 GLN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 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 ** 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: 0.7555 moved from start: 0.2783 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= 0.305 Angle : 0.683 9.761 13761 Z= 0.347 Chirality : 0.046 0.299 1497 Planarity : 0.005 0.067 1774 Dihedral : 13.829 108.042 1478 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 25.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % 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: -1.83 (0.46), residues: 83 sheet: -0.87 (0.31), residues: 274 loop : -1.21 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 415 HIS 0.009 0.002 HIS B 275 PHE 0.016 0.002 PHE B 241 TYR 0.014 0.002 TYR A 635 ARG 0.007 0.001 ARG B 277 *********************** 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 55 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6565 (mmtt) cc_final: 0.5989 (tppt) REVERT: A 508 MET cc_start: 0.9159 (mmm) cc_final: 0.8957 (mmp) REVERT: A 511 LEU cc_start: 0.9180 (tt) cc_final: 0.8630 (mt) REVERT: A 615 TYR cc_start: 0.8419 (m-80) cc_final: 0.8211 (m-80) REVERT: A 686 MET cc_start: 0.8552 (mtm) cc_final: 0.8278 (mtm) REVERT: B 278 ILE cc_start: 0.9517 (tt) cc_final: 0.9255 (pt) REVERT: B 294 MET cc_start: 0.8392 (tpt) cc_final: 0.7849 (tpt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.2196 time to fit residues: 18.2824 Evaluate side-chains 45 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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** A 343 ASN A 601 ASN B 54 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 10128 Z= 0.426 Angle : 0.802 9.167 13761 Z= 0.413 Chirality : 0.049 0.315 1497 Planarity : 0.006 0.055 1774 Dihedral : 14.022 108.286 1478 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 32.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % 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: -2.13 (0.23), residues: 1228 helix: -2.23 (0.43), residues: 88 sheet: -1.22 (0.32), residues: 261 loop : -1.45 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 415 HIS 0.008 0.002 HIS A 277 PHE 0.042 0.003 PHE A 344 TYR 0.018 0.002 TYR A 635 ARG 0.007 0.001 ARG B 266 *********************** 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 53 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.7346 (tpt) cc_final: 0.7129 (mmm) REVERT: A 686 MET cc_start: 0.8489 (mtm) cc_final: 0.8158 (mtm) REVERT: B 278 ILE cc_start: 0.9509 (tt) cc_final: 0.9274 (pt) REVERT: B 294 MET cc_start: 0.8500 (tpt) cc_final: 0.8018 (tpt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2211 time to fit residues: 17.6689 Evaluate side-chains 41 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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: 10.0000 chunk 13 optimal weight: 10.0000 chunk 68 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 119 optimal weight: 0.0060 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.2202 ------------------------------------------------------------------------------- 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 418 ASN A 601 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 202 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 478 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10128 Z= 0.191 Angle : 0.655 9.748 13761 Z= 0.327 Chirality : 0.047 0.350 1497 Planarity : 0.004 0.054 1774 Dihedral : 13.300 103.113 1478 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.09 % Allowed : 1.87 % Favored : 98.04 % 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: -1.67 (0.24), residues: 1228 helix: -1.61 (0.48), residues: 81 sheet: -0.95 (0.30), residues: 286 loop : -1.15 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 415 HIS 0.005 0.001 HIS B 275 PHE 0.013 0.002 PHE B 596 TYR 0.015 0.001 TYR B 41 ARG 0.013 0.001 ARG B 384 *********************** 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 67 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.7155 (tpt) cc_final: 0.6465 (tpp) REVERT: A 511 LEU cc_start: 0.9071 (tt) cc_final: 0.8505 (mt) REVERT: B 278 ILE cc_start: 0.9512 (tt) cc_final: 0.9279 (pt) REVERT: B 294 MET cc_start: 0.8376 (tpt) cc_final: 0.7822 (tpt) REVERT: B 478 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8603 (t0) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.2332 time to fit residues: 22.7028 Evaluate side-chains 45 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 44 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 0.0980 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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 601 ASN B 42 GLN B 45 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 202 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 ** 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: 0.7563 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10128 Z= 0.273 Angle : 0.674 8.729 13761 Z= 0.340 Chirality : 0.046 0.341 1497 Planarity : 0.005 0.110 1774 Dihedral : 13.126 103.991 1478 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.09 % Allowed : 2.24 % Favored : 97.67 % 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: -1.70 (0.24), residues: 1228 helix: -1.88 (0.46), residues: 87 sheet: -0.94 (0.31), residues: 272 loop : -1.15 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 188 HIS 0.005 0.001 HIS B 275 PHE 0.017 0.002 PHE A 536 TYR 0.011 0.002 TYR A 635 ARG 0.010 0.001 ARG B 331 *********************** 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 59 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6606 (mmtt) cc_final: 0.6103 (tppt) REVERT: A 339 MET cc_start: 0.7056 (tpt) cc_final: 0.6536 (tpp) REVERT: A 511 LEU cc_start: 0.9091 (tt) cc_final: 0.8518 (mt) REVERT: B 278 ILE cc_start: 0.9493 (tt) cc_final: 0.9258 (pt) REVERT: B 294 MET cc_start: 0.8372 (tpt) cc_final: 0.7857 (tpp) outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.2510 time to fit residues: 22.1691 Evaluate side-chains 45 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 418 ASN A 645 HIS ** 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10128 Z= 0.380 Angle : 0.770 8.827 13761 Z= 0.393 Chirality : 0.048 0.334 1497 Planarity : 0.006 0.080 1774 Dihedral : 13.344 104.733 1478 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: -2.00 (0.46), residues: 86 sheet: -1.08 (0.30), residues: 280 loop : -1.35 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 415 HIS 0.006 0.002 HIS A 243 PHE 0.024 0.002 PHE A 536 TYR 0.016 0.002 TYR A 635 ARG 0.010 0.001 ARG B 277 *********************** 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 52 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6616 (mmtt) cc_final: 0.6161 (tppt) REVERT: A 339 MET cc_start: 0.6988 (tpt) cc_final: 0.6492 (tpp) REVERT: A 511 LEU cc_start: 0.9133 (tt) cc_final: 0.8531 (mt) REVERT: B 294 MET cc_start: 0.8466 (tpt) cc_final: 0.7973 (tpt) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2231 time to fit residues: 17.5706 Evaluate side-chains 43 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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: 0.9980 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 60 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 418 ASN 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS ** 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: 0.7514 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10128 Z= 0.180 Angle : 0.650 9.006 13761 Z= 0.322 Chirality : 0.047 0.379 1497 Planarity : 0.005 0.061 1774 Dihedral : 12.583 99.115 1478 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.63 (0.24), residues: 1228 helix: -1.82 (0.47), residues: 87 sheet: -0.87 (0.31), residues: 284 loop : -1.10 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 415 HIS 0.005 0.001 HIS A 645 PHE 0.020 0.002 PHE B 46 TYR 0.011 0.001 TYR B 249 ARG 0.007 0.001 ARG B 331 ********************** 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 61 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LYS cc_start: 0.6519 (mmtt) cc_final: 0.6080 (tppt) REVERT: A 176 TYR cc_start: 0.8235 (m-80) cc_final: 0.7897 (m-80) REVERT: A 339 MET cc_start: 0.7118 (tpt) cc_final: 0.6662 (tpp) REVERT: A 511 LEU cc_start: 0.9093 (tt) cc_final: 0.8529 (mt) REVERT: B 294 MET cc_start: 0.8391 (tpt) cc_final: 0.8021 (tpt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.2079 time to fit residues: 19.3331 Evaluate side-chains 51 residues out of total 1119 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 ASN ** 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 528 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 = 0.3146 r_free = 0.3146 target = 0.037396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.032395 restraints weight = 120180.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.033133 restraints weight = 81744.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.033670 restraints weight = 60327.611| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10128 Z= 0.203 Angle : 0.631 8.442 13761 Z= 0.313 Chirality : 0.046 0.370 1497 Planarity : 0.005 0.056 1774 Dihedral : 12.161 99.592 1478 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -1.59 (0.24), residues: 1228 helix: -1.68 (0.48), residues: 87 sheet: -0.90 (0.30), residues: 285 loop : -1.07 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 617 HIS 0.007 0.001 HIS B 275 PHE 0.011 0.001 PHE B 535 TYR 0.013 0.001 TYR A 615 ARG 0.009 0.001 ARG B 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1736.23 seconds wall clock time: 32 minutes 50.89 seconds (1970.89 seconds total)