Starting phenix.real_space_refine (version: dev) on Tue Dec 13 16:21:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/12_2022/6w5r_21545_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6665 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 411": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 586": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 647": "NH1" <-> "NH2" Residue "A GLU 688": "OE1" <-> "OE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ARG 802": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9629 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1194, 9341 Classifications: {'peptide': 1194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 62, 'TRANS': 1130} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: "C" 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: 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 154 Unusual residues: {'CLR': 1, 'NAG': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.17, per 1000 atoms: 0.64 Number of scatterers: 9629 At special positions: 0 Unit cell: (105.83, 93.576, 155.96, 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 75 16.00 O 1806 8.00 N 1525 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.05 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.04 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.08 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=2.02 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.03 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.05 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 " NAG E 2 " - " MAN E 3 " BETA1-3 " NAG D 2 " - " BMA D 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1403 " - " ASN A 158 " " NAG A1404 " - " ASN A 452 " " NAG A1405 " - " ASN A 459 " " NAG A1408 " - " ASN A 524 " " NAG A1412 " - " ASN A 598 " " NAG A1413 " - " ASN A 916 " " NAG A1417 " - " ASN A 961 " " NAG A1418 " - " ASN A 968 " " NAG A1419 " - " ASN A1064 " " NAG B 1 " - " ASN A 222 " " NAG C 1 " - " ASN A 478 " " NAG D 1 " - " ASN A 557 " " NAG E 1 " - " ASN A 931 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 1.4 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 51.1% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.743A pdb=" N GLN A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.814A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix removed outlier: 5.173A pdb=" N ARG A 96 " --> pdb=" O GLN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 113 removed outlier: 3.825A pdb=" N GLU A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 150 through 160 removed outlier: 3.808A pdb=" N ALA A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.576A pdb=" N LEU A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 267 through 293 removed outlier: 4.018A pdb=" N TRP A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 348 removed outlier: 3.840A pdb=" N CYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.859A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 484 through 487 Processing helix chain 'A' and resid 492 through 495 No H-bonds generated for 'chain 'A' and resid 492 through 495' Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.899A pdb=" N ARG A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 575 through 592 removed outlier: 3.932A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 621 through 638 removed outlier: 4.165A pdb=" N ILE A 626 " --> pdb=" O PHE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 678 Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix removed outlier: 3.540A pdb=" N ASP A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 748 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 755 through 791 removed outlier: 4.715A pdb=" N VAL A 780 " --> pdb=" O ILE A 776 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 781 " --> pdb=" O THR A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 821 No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 832 through 851 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 994 through 1004 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1048 through 1069 Processing helix chain 'A' and resid 1083 through 1088 removed outlier: 4.164A pdb=" N VAL A1086 " --> pdb=" O VAL A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1121 through 1144 Processing helix chain 'A' and resid 1153 through 1176 removed outlier: 3.882A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1201 removed outlier: 4.301A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1213 Processing helix chain 'A' and resid 1219 through 1224 Processing helix chain 'A' and resid 1226 through 1251 Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 126 through 129 removed outlier: 3.802A pdb=" N GLU A 127 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.609A pdb=" N THR A 206 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 143 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 125 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= D, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1041 398 hydrogen bonds defined for protein. 1173 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: 3.01 Time building geometry restraints manager: 4.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1938 1.33 - 1.46: 2913 1.46 - 1.59: 4918 1.59 - 1.72: 4 1.72 - 1.85: 103 Bond restraints: 9876 Sorted by residual: bond pdb=" C THR A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.335 1.443 -0.109 1.28e-02 6.10e+03 7.24e+01 bond pdb=" C LEU A1244 " pdb=" N PRO A1245 " ideal model delta sigma weight residual 1.335 1.442 -0.107 1.38e-02 5.25e+03 5.96e+01 bond pdb=" C TYR A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 1.334 1.487 -0.153 2.34e-02 1.83e+03 4.28e+01 bond pdb=" CA SER A 602 " pdb=" CB SER A 602 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.51e-02 4.39e+03 3.58e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.426 1.572 -0.146 3.20e-02 9.77e+02 2.08e+01 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 80.27 - 91.84: 1 91.84 - 103.40: 120 103.40 - 114.97: 5692 114.97 - 126.54: 7424 126.54 - 138.11: 217 Bond angle restraints: 13454 Sorted by residual: angle pdb=" N ASN A 70 " pdb=" CA ASN A 70 " pdb=" C ASN A 70 " ideal model delta sigma weight residual 110.80 80.27 30.53 2.13e+00 2.20e-01 2.05e+02 angle pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 109.64 116.56 -6.92 5.38e-01 3.45e+00 1.65e+02 angle pdb=" C2 NAG A1404 " pdb=" N2 NAG A1404 " pdb=" C7 NAG A1404 " ideal model delta sigma weight residual 123.12 137.72 -14.60 1.28e+00 6.08e-01 1.29e+02 angle pdb=" C2 NAG A1412 " pdb=" N2 NAG A1412 " pdb=" C7 NAG A1412 " ideal model delta sigma weight residual 123.12 137.43 -14.31 1.28e+00 6.08e-01 1.24e+02 angle pdb=" C PRO A 48 " pdb=" N LYS A 49 " pdb=" CA LYS A 49 " ideal model delta sigma weight residual 120.49 134.59 -14.10 1.42e+00 4.96e-01 9.87e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.37: 5420 24.37 - 48.74: 329 48.74 - 73.12: 42 73.12 - 97.49: 9 97.49 - 121.86: 6 Dihedral angle restraints: 5806 sinusoidal: 2326 harmonic: 3480 Sorted by residual: dihedral pdb=" CA SER A 473 " pdb=" C SER A 473 " pdb=" N PRO A 474 " pdb=" CA PRO A 474 " ideal model delta harmonic sigma weight residual 0.00 41.59 -41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA ASN A 478 " pdb=" C ASN A 478 " pdb=" N CYS A 479 " pdb=" CA CYS A 479 " ideal model delta harmonic sigma weight residual 180.00 139.83 40.17 0 5.00e+00 4.00e-02 6.45e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual -86.00 -21.36 -64.64 1 1.00e+01 1.00e-02 5.49e+01 ... (remaining 5803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 1570 0.954 - 1.909: 2 1.909 - 2.863: 0 2.863 - 3.818: 0 3.818 - 4.772: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 2.37 -4.77 2.00e-02 2.50e+03 5.69e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-02 2.50e+03 6.85e+03 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-02 2.50e+03 4.84e+03 ... (remaining 1570 not shown) Planarity restraints: 1703 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.316 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.182 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " -0.086 2.00e-02 2.50e+03 7.12e-02 6.33e+01 pdb=" C7 NAG C 2 " 0.024 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " -0.065 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " 0.113 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 107 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.85e+01 pdb=" C LEU A 107 " -0.121 2.00e-02 2.50e+03 pdb=" O LEU A 107 " 0.045 2.00e-02 2.50e+03 pdb=" N PHE A 108 " 0.041 2.00e-02 2.50e+03 ... (remaining 1700 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 109 2.62 - 3.19: 7826 3.19 - 3.76: 14538 3.76 - 4.33: 19159 4.33 - 4.90: 32235 Nonbonded interactions: 73867 Sorted by model distance: nonbonded pdb=" O4 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.053 2.440 nonbonded pdb=" O ASP A 508 " pdb=" OG1 THR A 511 " model vdw 2.328 2.440 nonbonded pdb=" OG SER A 366 " pdb=" OH TYR A 677 " model vdw 2.341 2.440 nonbonded pdb=" O SER A 970 " pdb=" OG SER A 970 " model vdw 2.349 2.440 nonbonded pdb=" O ALA A1192 " pdb=" OG SER A1196 " model vdw 2.359 2.440 ... (remaining 73862 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 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'E' and resid 1 through 2) } 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 75 5.16 5 C 6223 2.51 5 N 1525 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 3.800 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.080 Process input model: 28.850 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.015 0.173 9876 Z= 0.967 Angle : 2.093 30.531 13454 Z= 1.224 Chirality : 0.178 4.772 1573 Planarity : 0.014 0.269 1690 Dihedral : 15.356 121.859 3523 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.73 % Favored : 92.59 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.27 % 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: -3.31 (0.21), residues: 1188 helix: -1.43 (0.18), residues: 617 sheet: -2.14 (0.60), residues: 75 loop : -3.18 (0.24), residues: 496 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.160 Fit side-chains outliers start: 40 outliers final: 16 residues processed: 181 average time/residue: 0.1838 time to fit residues: 48.7906 Evaluate side-chains 113 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.061 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.0888 time to fit residues: 4.1130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 56 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 103 ASN A 145 GLN A 185 ASN A 442 GLN A 465 GLN A 476 ASN A 581 GLN A 701 ASN A 707 GLN A 897 HIS A 905 GLN A 906 ASN A1016 HIS A1137 ASN A1193 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 9876 Z= 0.214 Angle : 0.754 12.819 13454 Z= 0.392 Chirality : 0.049 0.521 1573 Planarity : 0.005 0.043 1690 Dihedral : 9.767 107.073 1413 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.31 % Favored : 93.35 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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 (0.23), residues: 1188 helix: 0.06 (0.20), residues: 613 sheet: -1.94 (0.63), residues: 68 loop : -2.49 (0.25), residues: 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.134 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 140 average time/residue: 0.1646 time to fit residues: 36.0914 Evaluate side-chains 109 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.036 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.0905 time to fit residues: 3.3357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 96 optimal weight: 0.0870 chunk 107 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 GLN A 554 ASN A 581 GLN A 596 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN A1239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 9876 Z= 0.193 Angle : 0.683 10.453 13454 Z= 0.357 Chirality : 0.046 0.506 1573 Planarity : 0.004 0.040 1690 Dihedral : 9.581 108.477 1413 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.00 (0.24), residues: 1188 helix: 0.70 (0.21), residues: 612 sheet: -1.62 (0.59), residues: 71 loop : -2.31 (0.25), residues: 505 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.091 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 134 average time/residue: 0.1628 time to fit residues: 34.3873 Evaluate side-chains 112 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 1.049 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.0964 time to fit residues: 3.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.0050 chunk 11 optimal weight: 40.0000 chunk 51 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.4652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 9876 Z= 0.185 Angle : 0.646 10.124 13454 Z= 0.332 Chirality : 0.045 0.502 1573 Planarity : 0.004 0.054 1690 Dihedral : 9.467 108.726 1413 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.81 % Favored : 94.02 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.24), residues: 1188 helix: 0.93 (0.21), residues: 616 sheet: -1.13 (0.59), residues: 81 loop : -2.18 (0.25), residues: 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 100 time to evaluate : 1.074 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.1717 time to fit residues: 32.7669 Evaluate side-chains 107 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0953 time to fit residues: 3.6475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 9876 Z= 0.190 Angle : 0.632 10.103 13454 Z= 0.326 Chirality : 0.046 0.503 1573 Planarity : 0.004 0.054 1690 Dihedral : 9.417 109.072 1413 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.35 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1188 helix: 1.11 (0.22), residues: 617 sheet: -0.98 (0.59), residues: 81 loop : -2.05 (0.26), residues: 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 116 average time/residue: 0.1588 time to fit residues: 28.6528 Evaluate side-chains 104 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.976 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.0880 time to fit residues: 2.6667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 9876 Z= 0.242 Angle : 0.661 9.771 13454 Z= 0.338 Chirality : 0.046 0.514 1573 Planarity : 0.004 0.041 1690 Dihedral : 9.409 108.462 1413 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.73 % Favored : 93.01 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1188 helix: 1.13 (0.22), residues: 613 sheet: -0.81 (0.60), residues: 79 loop : -1.93 (0.27), residues: 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 107 average time/residue: 0.1693 time to fit residues: 28.4559 Evaluate side-chains 101 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 1.160 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.0908 time to fit residues: 3.1362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9876 Z= 0.217 Angle : 0.634 9.974 13454 Z= 0.326 Chirality : 0.045 0.498 1573 Planarity : 0.004 0.058 1690 Dihedral : 9.384 108.903 1413 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1188 helix: 1.14 (0.22), residues: 614 sheet: -0.72 (0.60), residues: 79 loop : -1.86 (0.27), residues: 495 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 107 average time/residue: 0.1840 time to fit residues: 30.6680 Evaluate side-chains 99 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.037 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.0956 time to fit residues: 3.2537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9876 Z= 0.196 Angle : 0.624 10.054 13454 Z= 0.321 Chirality : 0.045 0.490 1573 Planarity : 0.004 0.057 1690 Dihedral : 9.350 109.111 1413 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1188 helix: 1.17 (0.22), residues: 612 sheet: -0.61 (0.61), residues: 79 loop : -1.84 (0.27), residues: 497 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.1770 time to fit residues: 28.1280 Evaluate side-chains 96 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 91 time to evaluate : 1.011 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0931 time to fit residues: 2.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 68 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 556 ASN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9876 Z= 0.204 Angle : 0.627 9.952 13454 Z= 0.324 Chirality : 0.045 0.487 1573 Planarity : 0.004 0.057 1690 Dihedral : 9.359 109.072 1413 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.35 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1188 helix: 1.20 (0.22), residues: 610 sheet: -0.53 (0.62), residues: 79 loop : -1.86 (0.27), residues: 499 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 93 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 100 average time/residue: 0.1808 time to fit residues: 28.3696 Evaluate side-chains 95 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 1.107 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0980 time to fit residues: 2.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 9876 Z= 0.193 Angle : 0.633 13.171 13454 Z= 0.324 Chirality : 0.045 0.480 1573 Planarity : 0.004 0.056 1690 Dihedral : 9.344 109.140 1413 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.48 % Favored : 93.43 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1188 helix: 1.29 (0.22), residues: 603 sheet: -0.45 (0.63), residues: 79 loop : -1.84 (0.26), residues: 506 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 93 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1786 time to fit residues: 26.3721 Evaluate side-chains 92 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 1.156 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1059 time to fit residues: 1.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.166906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127892 restraints weight = 13650.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127622 restraints weight = 8730.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.128622 restraints weight = 8575.852| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 9876 Z= 0.242 Angle : 0.651 9.732 13454 Z= 0.336 Chirality : 0.046 0.492 1573 Planarity : 0.004 0.054 1690 Dihedral : 9.372 108.802 1413 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.65 % Favored : 93.18 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1188 helix: 1.19 (0.22), residues: 610 sheet: -0.41 (0.62), residues: 79 loop : -1.85 (0.27), residues: 499 =============================================================================== Job complete usr+sys time: 1678.65 seconds wall clock time: 31 minutes 45.14 seconds (1905.14 seconds total)