Starting phenix.real_space_refine (version: dev) on Sat Feb 18 06:02:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3x_32295/02_2023/7w3x_32295.pdb" } resolution = 3.21 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 782": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7429 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 7025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7025 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 855} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 4.80, per 1000 atoms: 0.65 Number of scatterers: 7429 At special positions: 0 Unit cell: (100.885, 93.0579, 130.455, 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 32 16.00 O 1489 8.00 N 1199 7.00 C 4709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 621 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS C 742 " - pdb=" SG CYS C 764 " 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 ALPHA1-2 " MAN A 5 " - " MAN A 6 " ALPHA1-3 " BMA A 3 " - " MAN A 8 " " MAN A 4 " - " MAN A 7 " " BMA D 3 " - " MAN D 4 " ALPHA1-6 " BMA A 3 " - " MAN A 4 " " MAN A 4 " - " MAN A 5 " " BMA D 3 " - " MAN D 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A 1 " - " ASN C 143 " " NAG B 1 " - " ASN C 311 " " NAG C1001 " - " ASN C 73 " " NAG C1002 " - " ASN C 159 " " NAG C1003 " - " ASN C 234 " " NAG C1004 " - " ASN C 261 " " NAG C1005 " - " ASN C 481 " " NAG C1006 " - " ASN C 532 " " NAG C1007 " - " ASN C 542 " " NAG C1008 " - " ASN C 591 " " NAG C1009 " - " ASN C 767 " " NAG C1010 " - " ASN C 888 " " NAG C1011 " - " ASN C 855 " " NAG D 1 " - " ASN C 562 " " NAG E 1 " - " ASN C 647 " " NAG F 1 " - " ASN C 848 " Time building additional restraints: 3.80 Conformation dependent library (CDL) restraints added in 962.7 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 20.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 31 through 44 removed outlier: 3.659A pdb=" N GLY C 44 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.850A pdb=" N LEU C 108 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 109 " --> pdb=" O PRO C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.703A pdb=" N PHE C 136 " --> pdb=" O ILE C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.734A pdb=" N LYS C 158 " --> pdb=" O THR C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 183 removed outlier: 3.502A pdb=" N SER C 182 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 removed outlier: 3.567A pdb=" N GLU C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 256 through 262 Processing helix chain 'C' and resid 281 through 285 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.607A pdb=" N GLY C 310 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 311 " --> pdb=" O SER C 308 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 312 " --> pdb=" O PHE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 428 through 434 removed outlier: 3.778A pdb=" N GLY C 432 " --> pdb=" O GLN C 429 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 434 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 457 removed outlier: 3.726A pdb=" N MET C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 455 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 3.878A pdb=" N SER C 480 " --> pdb=" O SER C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.717A pdb=" N LEU C 527 " --> pdb=" O PRO C 524 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN C 528 " --> pdb=" O LYS C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 644 through 648 Processing helix chain 'C' and resid 666 through 672 removed outlier: 3.848A pdb=" N GLY C 670 " --> pdb=" O GLN C 667 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 672 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 719 removed outlier: 3.718A pdb=" N THR C 718 " --> pdb=" O ALA C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 745 removed outlier: 3.802A pdb=" N LEU C 744 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 745 " --> pdb=" O CYS C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 768 Processing helix chain 'C' and resid 802 through 811 Processing helix chain 'C' and resid 861 through 865 Processing helix chain 'C' and resid 883 through 889 Processing helix chain 'C' and resid 917 through 921 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 46 removed outlier: 4.164A pdb=" N THR C 101 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 70 through 72 removed outlier: 6.485A pdb=" N GLU C 71 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE C 80 " --> pdb=" O PHE C 116 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ASP C 118 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU C 82 " --> pdb=" O ASP C 118 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 190 " --> pdb=" O ASP C 216 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 215 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 243 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 269 " --> pdb=" O ASN C 294 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU C 293 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU C 393 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 488 " --> pdb=" O ASN C 513 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU C 561 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE C 585 " --> pdb=" O TYR C 607 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE C 606 " --> pdb=" O ASP C 631 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 654 " --> pdb=" O TYR C 679 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 726 " --> pdb=" O ASP C 751 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU C 750 " --> pdb=" O ASP C 824 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE C 823 " --> pdb=" O ASN C 848 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 151 removed outlier: 4.158A pdb=" N GLY C 151 " --> pdb=" O ASN C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 327 through 328 removed outlier: 5.969A pdb=" N GLN C 327 " --> pdb=" O PHE C 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 357 through 358 removed outlier: 6.544A pdb=" N LEU C 357 " --> pdb=" O MET C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 377 through 378 removed outlier: 7.293A pdb=" N GLN C 399 " --> pdb=" O GLY C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 569 through 570 removed outlier: 3.928A pdb=" N GLY C 570 " --> pdb=" O ASN C 591 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 614 through 616 removed outlier: 5.537A pdb=" N GLY C 615 " --> pdb=" O SER C 638 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 687 through 688 removed outlier: 5.958A pdb=" N GLY C 687 " --> pdb=" O THR C 709 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ARG C 711 " --> pdb=" O GLY C 687 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU C 708 " --> pdb=" O LYS C 732 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C 734 " --> pdb=" O LEU C 708 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 710 " --> pdb=" O TYR C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 758 through 759 removed outlier: 3.707A pdb=" N GLY C 759 " --> pdb=" O LYS C 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 782 through 788 Processing sheet with id=AB3, first strand: chain 'C' and resid 855 through 856 removed outlier: 4.920A pdb=" N GLY C 856 " --> pdb=" O SER C 879 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU C 878 " --> pdb=" O HIS C 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 870 through 872 removed outlier: 6.953A pdb=" N LEU C 871 " --> pdb=" O ASP C 896 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 104 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 3.78 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: 2327 1.34 - 1.46: 1499 1.46 - 1.58: 3698 1.58 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 7572 Sorted by residual: bond pdb=" CA THR C 101 " pdb=" CB THR C 101 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.35e-02 5.49e+03 2.72e+00 bond pdb=" C1 NAG C1004 " pdb=" C2 NAG C1004 " ideal model delta sigma weight residual 1.526 1.551 -0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" CG ASN C 261 " pdb=" ND2 ASN C 261 " ideal model delta sigma weight residual 1.328 1.353 -0.025 2.10e-02 2.27e+03 1.42e+00 bond pdb=" CB ASN C 261 " pdb=" CG ASN C 261 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.36e+00 bond pdb=" CA ASN C 261 " pdb=" CB ASN C 261 " ideal model delta sigma weight residual 1.528 1.543 -0.015 1.35e-02 5.49e+03 1.29e+00 ... (remaining 7567 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 217 106.78 - 113.57: 4329 113.57 - 120.37: 2601 120.37 - 127.17: 3040 127.17 - 133.96: 68 Bond angle restraints: 10255 Sorted by residual: angle pdb=" N VAL C 486 " pdb=" CA VAL C 486 " pdb=" C VAL C 486 " ideal model delta sigma weight residual 113.20 109.87 3.33 9.60e-01 1.09e+00 1.20e+01 angle pdb=" N ILE C 538 " pdb=" CA ILE C 538 " pdb=" C ILE C 538 " ideal model delta sigma weight residual 111.77 108.26 3.51 1.04e+00 9.25e-01 1.14e+01 angle pdb=" CA GLU C 123 " pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " ideal model delta sigma weight residual 114.10 120.38 -6.28 2.00e+00 2.50e-01 9.86e+00 angle pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " pdb=" C5 NAG B 2 " ideal model delta sigma weight residual 113.34 118.48 -5.14 1.74e+00 3.30e-01 8.73e+00 angle pdb=" C TRP C 67 " pdb=" CA TRP C 67 " pdb=" CB TRP C 67 " ideal model delta sigma weight residual 109.80 112.86 -3.06 1.23e+00 6.61e-01 6.19e+00 ... (remaining 10250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 4212 21.38 - 42.76: 303 42.76 - 64.15: 19 64.15 - 85.53: 10 85.53 - 106.91: 9 Dihedral angle restraints: 4553 sinusoidal: 1974 harmonic: 2579 Sorted by residual: dihedral pdb=" CB CYS C 90 " pdb=" SG CYS C 90 " pdb=" SG CYS C 95 " pdb=" CB CYS C 95 " ideal model delta sinusoidal sigma weight residual -86.00 -162.81 76.81 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS C 621 " pdb=" SG CYS C 621 " pdb=" SG CYS C 644 " pdb=" CB CYS C 644 " ideal model delta sinusoidal sigma weight residual 93.00 17.31 75.69 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CA ASN C 261 " pdb=" C ASN C 261 " pdb=" N PHE C 262 " pdb=" CA PHE C 262 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 4550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 959 0.051 - 0.101: 243 0.101 - 0.152: 44 0.152 - 0.202: 6 0.202 - 0.253: 1 Chirality restraints: 1253 Sorted by residual: chirality pdb=" C1 NAG C1011 " pdb=" ND2 ASN C 855 " pdb=" C2 NAG C1011 " pdb=" O5 NAG C1011 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG C1005 " pdb=" ND2 ASN C 481 " pdb=" C2 NAG C1005 " pdb=" O5 NAG C1005 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CB ILE C 882 " pdb=" CA ILE C 882 " pdb=" CG1 ILE C 882 " pdb=" CG2 ILE C 882 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1250 not shown) Planarity restraints: 1286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 67 " -0.042 2.00e-02 2.50e+03 3.93e-02 3.87e+01 pdb=" CG TRP C 67 " 0.105 2.00e-02 2.50e+03 pdb=" CD1 TRP C 67 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP C 67 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP C 67 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 67 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 67 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 67 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 67 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP C 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 767 " 0.005 2.00e-02 2.50e+03 2.38e-02 7.06e+00 pdb=" CG ASN C 767 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 767 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN C 767 " -0.025 2.00e-02 2.50e+03 pdb=" C1 NAG C1009 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 261 " -0.002 2.00e-02 2.50e+03 1.62e-02 3.30e+00 pdb=" CG ASN C 261 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 261 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 261 " 0.017 2.00e-02 2.50e+03 pdb=" C1 NAG C1004 " -0.016 2.00e-02 2.50e+03 ... (remaining 1283 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 472 2.73 - 3.27: 7470 3.27 - 3.82: 11515 3.82 - 4.36: 14467 4.36 - 4.90: 24164 Nonbonded interactions: 58088 Sorted by model distance: nonbonded pdb=" O PHE C 260 " pdb=" OG SER C 263 " model vdw 2.190 2.440 nonbonded pdb=" OD1 ASP C 394 " pdb=" OG SER C 396 " model vdw 2.254 2.440 nonbonded pdb=" OE1 GLU C 461 " pdb=" OH TYR C 792 " model vdw 2.255 2.440 nonbonded pdb=" OG SER C 46 " pdb=" O THR C 101 " model vdw 2.264 2.440 nonbonded pdb=" O4 NAG C1011 " pdb=" O7 NAG C1011 " model vdw 2.285 2.440 ... (remaining 58083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } 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 32 5.16 5 C 4709 2.51 5 N 1199 2.21 5 O 1489 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.500 Check model and map are aligned: 0.110 Process input model: 23.310 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7572 Z= 0.216 Angle : 0.634 7.212 10255 Z= 0.344 Chirality : 0.046 0.253 1253 Planarity : 0.004 0.044 1270 Dihedral : 14.349 106.909 2877 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.28), residues: 889 helix: -2.51 (0.40), residues: 145 sheet: -2.57 (0.39), residues: 169 loop : -1.63 (0.26), residues: 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1945 time to fit residues: 57.1658 Evaluate side-chains 195 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.916 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.0000 chunk 80 optimal weight: 1.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 809 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7572 Z= 0.204 Angle : 0.599 7.048 10255 Z= 0.307 Chirality : 0.046 0.271 1253 Planarity : 0.004 0.040 1270 Dihedral : 9.799 106.888 1172 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.82 (0.27), residues: 889 helix: -2.43 (0.42), residues: 133 sheet: -2.62 (0.39), residues: 170 loop : -1.52 (0.25), residues: 586 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 206 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 209 average time/residue: 0.2044 time to fit residues: 57.5097 Evaluate side-chains 201 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0922 time to fit residues: 2.1661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7572 Z= 0.191 Angle : 0.582 7.824 10255 Z= 0.297 Chirality : 0.045 0.263 1253 Planarity : 0.004 0.038 1270 Dihedral : 9.736 106.955 1172 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.28), residues: 889 helix: -2.47 (0.41), residues: 139 sheet: -2.55 (0.39), residues: 175 loop : -1.50 (0.26), residues: 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 201 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 204 average time/residue: 0.2008 time to fit residues: 54.9983 Evaluate side-chains 199 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 194 time to evaluate : 0.836 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0737 time to fit residues: 1.8254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7572 Z= 0.172 Angle : 0.563 6.966 10255 Z= 0.291 Chirality : 0.045 0.274 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.710 107.045 1172 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.27), residues: 889 helix: -2.49 (0.41), residues: 140 sheet: -2.52 (0.39), residues: 175 loop : -1.52 (0.26), residues: 574 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 203 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 206 average time/residue: 0.1974 time to fit residues: 54.6324 Evaluate side-chains 197 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0806 time to fit residues: 1.8153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 0.0030 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN C 327 GLN C 565 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7572 Z= 0.262 Angle : 0.607 7.504 10255 Z= 0.311 Chirality : 0.047 0.272 1253 Planarity : 0.004 0.037 1270 Dihedral : 9.768 107.000 1172 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.28), residues: 889 helix: -2.43 (0.42), residues: 139 sheet: -2.57 (0.38), residues: 181 loop : -1.51 (0.26), residues: 569 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 207 average time/residue: 0.1965 time to fit residues: 54.8768 Evaluate side-chains 200 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 0.863 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0710 time to fit residues: 1.8323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 GLN C 513 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 7572 Z= 0.196 Angle : 0.606 8.330 10255 Z= 0.315 Chirality : 0.061 1.391 1253 Planarity : 0.004 0.036 1270 Dihedral : 9.744 106.917 1172 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.27), residues: 889 helix: -2.62 (0.39), residues: 153 sheet: -2.60 (0.42), residues: 150 loop : -1.79 (0.26), residues: 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 200 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 206 average time/residue: 0.2004 time to fit residues: 55.4445 Evaluate side-chains 200 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0685 time to fit residues: 2.0674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 7572 Z= 0.185 Angle : 0.587 7.598 10255 Z= 0.305 Chirality : 0.049 0.654 1253 Planarity : 0.003 0.035 1270 Dihedral : 9.665 106.940 1172 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.28), residues: 889 helix: -2.49 (0.40), residues: 147 sheet: -2.59 (0.43), residues: 145 loop : -1.67 (0.26), residues: 597 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 200 average time/residue: 0.2028 time to fit residues: 54.2956 Evaluate side-chains 202 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 195 time to evaluate : 0.894 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0745 time to fit residues: 2.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 67 optimal weight: 0.1980 chunk 78 optimal weight: 5.9990 chunk 82 optimal weight: 0.0870 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 ASN C 198 GLN C 274 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7572 Z= 0.161 Angle : 0.591 9.623 10255 Z= 0.303 Chirality : 0.045 0.365 1253 Planarity : 0.003 0.035 1270 Dihedral : 9.608 106.988 1172 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.28), residues: 889 helix: -2.36 (0.42), residues: 137 sheet: -2.44 (0.44), residues: 142 loop : -1.58 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 201 average time/residue: 0.2196 time to fit residues: 59.3096 Evaluate side-chains 197 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 195 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0739 time to fit residues: 1.5379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN ** C 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 7572 Z= 0.231 Angle : 0.618 8.456 10255 Z= 0.318 Chirality : 0.046 0.372 1253 Planarity : 0.004 0.035 1270 Dihedral : 9.653 106.966 1172 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.28), residues: 889 helix: -2.39 (0.42), residues: 139 sheet: -2.52 (0.43), residues: 150 loop : -1.58 (0.26), residues: 600 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 203 average time/residue: 0.2130 time to fit residues: 58.1386 Evaluate side-chains 201 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0753 time to fit residues: 1.6337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.4980 chunk 81 optimal weight: 0.0270 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 0.0570 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 530 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 7572 Z= 0.182 Angle : 0.623 8.386 10255 Z= 0.321 Chirality : 0.045 0.306 1253 Planarity : 0.004 0.034 1270 Dihedral : 9.638 106.928 1172 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.28), residues: 889 helix: -2.25 (0.44), residues: 131 sheet: -2.35 (0.44), residues: 142 loop : -1.63 (0.25), residues: 616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 199 average time/residue: 0.2061 time to fit residues: 54.9613 Evaluate side-chains 193 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0908 time to fit residues: 1.3894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 198 GLN C 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.106178 restraints weight = 10843.579| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.45 r_work: 0.3249 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 7572 Z= 0.198 Angle : 0.621 8.593 10255 Z= 0.318 Chirality : 0.046 0.253 1253 Planarity : 0.004 0.034 1270 Dihedral : 9.628 106.999 1172 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.28), residues: 889 helix: -2.29 (0.43), residues: 133 sheet: -2.46 (0.38), residues: 191 loop : -1.32 (0.27), residues: 565 =============================================================================== Job complete usr+sys time: 2209.10 seconds wall clock time: 40 minutes 40.84 seconds (2440.84 seconds total)