Starting phenix.real_space_refine on Fri Feb 16 19:04:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/02_2024/6w5r_21545_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/02_2024/6w5r_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_21545/02_2024/6w5r_21545.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/02_2024/6w5r_21545.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/02_2024/6w5r_21545_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5r_21545/02_2024/6w5r_21545_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 6 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 dihedrals: 6 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: 9 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: 9 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.43, per 1000 atoms: 0.56 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: 5.07 Conformation dependent library (CDL) restraints added in 1.7 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: 2.50 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: 2.93 Time building geometry restraints manager: 4.42 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=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.572 -0.166 2.00e-02 2.50e+03 6.88e+01 bond pdb=" C1 NAG A1413 " pdb=" O5 NAG A1413 " ideal model delta sigma weight residual 1.406 1.561 -0.155 2.00e-02 2.50e+03 5.99e+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 ... (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=" 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 angle pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" C VAL A 71 " ideal model delta sigma weight residual 110.53 118.55 -8.02 9.40e-01 1.13e+00 7.28e+01 angle pdb=" N PRO A 939 " pdb=" CA PRO A 939 " pdb=" C PRO A 939 " ideal model delta sigma weight residual 113.53 124.66 -11.13 1.39e+00 5.18e-01 6.41e+01 angle pdb=" CA CYS A 177 " pdb=" CB CYS A 177 " pdb=" SG CYS A 177 " ideal model delta sigma weight residual 114.40 131.61 -17.21 2.30e+00 1.89e-01 5.60e+01 ... (remaining 13449 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.96: 5772 26.96 - 53.93: 286 53.93 - 80.89: 43 80.89 - 107.86: 24 107.86 - 134.82: 10 Dihedral angle restraints: 6135 sinusoidal: 2655 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 6132 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 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: 0.620 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: 3.480 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.030 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 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= 0.983 Angle : 2.102 30.531 13454 Z= 1.200 Chirality : 0.179 4.772 1573 Planarity : 0.014 0.269 1690 Dihedral : 17.453 134.819 3852 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 % Allowed : 8.41 % Favored : 87.73 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP A 833 HIS 0.026 0.005 HIS A1042 PHE 0.054 0.007 PHE A 108 TYR 0.046 0.007 TYR A 157 ARG 0.019 0.002 ARG A 789 *********************** 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 : 1.030 Fit side-chains REVERT: A 220 MET cc_start: 0.2696 (ppp) cc_final: 0.2254 (ptm) REVERT: A 272 MET cc_start: 0.6926 (mmp) cc_final: 0.6707 (mmp) REVERT: A 436 ASP cc_start: 0.6657 (OUTLIER) cc_final: 0.6396 (m-30) REVERT: A 622 PHE cc_start: 0.6364 (t80) cc_final: 0.5641 (m-10) REVERT: A 633 LEU cc_start: 0.8508 (tp) cc_final: 0.8301 (tp) REVERT: A 1089 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7533 (tp30) outliers start: 40 outliers final: 16 residues processed: 181 average time/residue: 0.1988 time to fit residues: 52.0890 Evaluate side-chains 115 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1089 GLU Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1169 SER 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: 0.7980 chunk 48 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 0.1980 chunk 69 optimal weight: 0.9980 chunk 108 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 41 ASN ** A 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7312 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9876 Z= 0.208 Angle : 0.814 12.742 13454 Z= 0.389 Chirality : 0.049 0.354 1573 Planarity : 0.005 0.042 1690 Dihedral : 13.368 93.161 1769 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.48 % Favored : 93.27 % Rotamer: Outliers : 3.19 % Allowed : 14.20 % Favored : 82.61 % 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: -1.60 (0.23), residues: 1188 helix: 0.10 (0.21), residues: 613 sheet: -1.40 (0.69), residues: 58 loop : -2.50 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 291 HIS 0.008 0.001 HIS A1029 PHE 0.020 0.002 PHE A 345 TYR 0.014 0.002 TYR A 269 ARG 0.005 0.001 ARG A 78 *********************** 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 150 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 117 time to evaluate : 0.985 Fit side-chains REVERT: A 145 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4844 (pp30) REVERT: A 220 MET cc_start: 0.2443 (ppp) cc_final: 0.1579 (ptm) REVERT: A 436 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6582 (m-30) REVERT: A 622 PHE cc_start: 0.6546 (t80) cc_final: 0.5838 (m-10) REVERT: A 769 PHE cc_start: 0.8619 (t80) cc_final: 0.8319 (t80) REVERT: A 1114 MET cc_start: 0.6895 (tmm) cc_final: 0.6627 (tmm) REVERT: A 1133 MET cc_start: 0.7218 (ttm) cc_final: 0.6987 (mtp) REVERT: A 1137 ASN cc_start: 0.8139 (m-40) cc_final: 0.7898 (m110) REVERT: A 1197 SER cc_start: 0.8899 (m) cc_final: 0.8512 (t) outliers start: 33 outliers final: 18 residues processed: 145 average time/residue: 0.1659 time to fit residues: 37.2465 Evaluate side-chains 122 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 676 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1179 MET Chi-restraints excluded: chain A residue 1198 VAL 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: 0.3980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.0010 chunk 107 optimal weight: 0.4980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 581 GLN A 596 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9876 Z= 0.177 Angle : 0.736 11.321 13454 Z= 0.348 Chirality : 0.046 0.303 1573 Planarity : 0.004 0.040 1690 Dihedral : 10.999 76.471 1754 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 3.96 % Allowed : 15.65 % Favored : 80.39 % 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: -0.93 (0.24), residues: 1188 helix: 0.73 (0.21), residues: 618 sheet: -1.59 (0.59), residues: 71 loop : -2.26 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 291 HIS 0.006 0.001 HIS A1042 PHE 0.021 0.001 PHE A 345 TYR 0.016 0.001 TYR A 457 ARG 0.002 0.000 ARG A 39 *********************** 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 154 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5713 (t80) REVERT: A 349 ASN cc_start: 0.7784 (m-40) cc_final: 0.7511 (m110) REVERT: A 436 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6385 (m-30) REVERT: A 551 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8175 (p0) REVERT: A 622 PHE cc_start: 0.6506 (t80) cc_final: 0.5746 (m-10) REVERT: A 633 LEU cc_start: 0.8457 (tp) cc_final: 0.8235 (tp) REVERT: A 1114 MET cc_start: 0.6737 (tmm) cc_final: 0.6353 (tmm) REVERT: A 1133 MET cc_start: 0.7091 (ttm) cc_final: 0.6883 (mtp) REVERT: A 1137 ASN cc_start: 0.8134 (m-40) cc_final: 0.7831 (m110) outliers start: 41 outliers final: 25 residues processed: 149 average time/residue: 0.1657 time to fit residues: 39.0027 Evaluate side-chains 127 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1145 TRP Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 106 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 30.0000 chunk 51 optimal weight: 0.0010 chunk 72 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7309 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9876 Z= 0.175 Angle : 0.683 10.017 13454 Z= 0.325 Chirality : 0.045 0.284 1573 Planarity : 0.004 0.052 1690 Dihedral : 9.682 71.781 1752 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 4.25 % Allowed : 16.33 % Favored : 79.42 % 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: -0.60 (0.24), residues: 1188 helix: 1.00 (0.22), residues: 617 sheet: -1.12 (0.59), residues: 81 loop : -2.18 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 833 HIS 0.006 0.001 HIS A1042 PHE 0.028 0.001 PHE A 769 TYR 0.011 0.001 TYR A1037 ARG 0.001 0.000 ARG A 958 *********************** 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 149 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 105 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.5516 (t80) REVERT: A 349 ASN cc_start: 0.7577 (m-40) cc_final: 0.6937 (t0) REVERT: A 551 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8224 (p0) REVERT: A 622 PHE cc_start: 0.6635 (t80) cc_final: 0.5797 (m-10) REVERT: A 661 ILE cc_start: 0.7568 (mm) cc_final: 0.7265 (mm) REVERT: A 872 MET cc_start: 0.7871 (mmm) cc_final: 0.7483 (mmt) REVERT: A 1114 MET cc_start: 0.6788 (tmm) cc_final: 0.6216 (tmm) REVERT: A 1133 MET cc_start: 0.7110 (ttm) cc_final: 0.6904 (mtp) REVERT: A 1137 ASN cc_start: 0.8113 (m-40) cc_final: 0.7868 (m110) REVERT: A 1220 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6917 (tp) outliers start: 44 outliers final: 28 residues processed: 144 average time/residue: 0.1471 time to fit residues: 33.5138 Evaluate side-chains 130 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 99 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 889 VAL Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 85 optimal weight: 0.0980 chunk 47 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 79 optimal weight: 0.0470 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 overall best weight: 0.2836 ------------------------------------------------------------------------------- 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** A1156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9876 Z= 0.152 Angle : 0.645 10.110 13454 Z= 0.308 Chirality : 0.043 0.272 1573 Planarity : 0.004 0.053 1690 Dihedral : 8.641 67.257 1748 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.14 % Favored : 93.60 % Rotamer: Outliers : 3.67 % Allowed : 17.97 % Favored : 78.36 % 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: -0.27 (0.25), residues: 1188 helix: 1.22 (0.22), residues: 611 sheet: -0.78 (0.60), residues: 79 loop : -1.93 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 833 HIS 0.005 0.001 HIS A1042 PHE 0.025 0.001 PHE A 736 TYR 0.015 0.001 TYR A 457 ARG 0.001 0.000 ARG A 116 *********************** 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 143 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 105 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 288 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.5469 (t80) REVERT: A 349 ASN cc_start: 0.7447 (m-40) cc_final: 0.6869 (t0) REVERT: A 551 ASP cc_start: 0.8515 (OUTLIER) cc_final: 0.8231 (p0) REVERT: A 633 LEU cc_start: 0.8403 (tp) cc_final: 0.8151 (tp) REVERT: A 661 ILE cc_start: 0.7580 (mm) cc_final: 0.7335 (mm) REVERT: A 872 MET cc_start: 0.7938 (mmm) cc_final: 0.7580 (mmt) REVERT: A 1114 MET cc_start: 0.6723 (tmm) cc_final: 0.6115 (tmm) REVERT: A 1220 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6796 (tp) outliers start: 38 outliers final: 27 residues processed: 141 average time/residue: 0.1643 time to fit residues: 36.4042 Evaluate side-chains 132 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- 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** A1156 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.180 Angle : 0.656 9.825 13454 Z= 0.312 Chirality : 0.044 0.272 1573 Planarity : 0.004 0.040 1690 Dihedral : 7.999 63.663 1748 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.98 % Favored : 93.86 % Rotamer: Outliers : 4.06 % Allowed : 18.74 % Favored : 77.20 % 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: -0.13 (0.25), residues: 1188 helix: 1.29 (0.22), residues: 612 sheet: -0.68 (0.59), residues: 79 loop : -1.81 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 833 HIS 0.008 0.001 HIS A1042 PHE 0.021 0.001 PHE A 632 TYR 0.013 0.001 TYR A1037 ARG 0.002 0.000 ARG A1173 *********************** 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 144 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 102 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASN cc_start: 0.7464 (m-40) cc_final: 0.6978 (t0) REVERT: A 436 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6326 (m-30) REVERT: A 551 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8245 (p0) REVERT: A 622 PHE cc_start: 0.6373 (t80) cc_final: 0.5586 (m-10) REVERT: A 661 ILE cc_start: 0.7629 (mm) cc_final: 0.7382 (mm) REVERT: A 677 TYR cc_start: 0.6410 (t80) cc_final: 0.6031 (t80) REVERT: A 872 MET cc_start: 0.7940 (mmm) cc_final: 0.7529 (mmm) REVERT: A 1114 MET cc_start: 0.6770 (tmm) cc_final: 0.6103 (tmm) REVERT: A 1159 MET cc_start: 0.7974 (ttm) cc_final: 0.7749 (ttp) REVERT: A 1220 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6910 (tp) outliers start: 42 outliers final: 32 residues processed: 136 average time/residue: 0.1533 time to fit residues: 32.8345 Evaluate side-chains 132 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 642 MET Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 950 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE 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: 0.7980 chunk 84 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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** A 925 ASN A1101 ASN A1239 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9876 Z= 0.372 Angle : 0.777 9.639 13454 Z= 0.379 Chirality : 0.049 0.301 1573 Planarity : 0.005 0.056 1690 Dihedral : 8.142 60.490 1748 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.32 % Favored : 92.42 % Rotamer: Outliers : 4.64 % Allowed : 18.65 % Favored : 76.71 % 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: -0.52 (0.25), residues: 1188 helix: 0.99 (0.22), residues: 613 sheet: -1.00 (0.57), residues: 79 loop : -2.01 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 260 HIS 0.009 0.001 HIS A1042 PHE 0.023 0.002 PHE A 736 TYR 0.023 0.002 TYR A1037 ARG 0.004 0.001 ARG A 411 *********************** 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 144 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 96 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 145 GLN cc_start: 0.5128 (OUTLIER) cc_final: 0.4867 (pp30) REVERT: A 349 ASN cc_start: 0.7620 (m-40) cc_final: 0.7131 (t0) REVERT: A 436 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: A 622 PHE cc_start: 0.6499 (t80) cc_final: 0.5771 (m-10) REVERT: A 1114 MET cc_start: 0.6929 (tmm) cc_final: 0.6244 (tmm) REVERT: A 1137 ASN cc_start: 0.8091 (m-40) cc_final: 0.7828 (m110) REVERT: A 1220 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7132 (tp) outliers start: 48 outliers final: 37 residues processed: 134 average time/residue: 0.1542 time to fit residues: 32.5102 Evaluate side-chains 130 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 90 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 574 THR Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 797 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 948 ASP Chi-restraints excluded: chain A residue 1036 THR Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7358 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9876 Z= 0.180 Angle : 0.668 10.182 13454 Z= 0.318 Chirality : 0.044 0.285 1573 Planarity : 0.004 0.056 1690 Dihedral : 7.817 58.420 1748 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.72 % Favored : 94.02 % Rotamer: Outliers : 3.38 % Allowed : 21.16 % Favored : 75.46 % 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: -0.32 (0.25), residues: 1188 helix: 1.15 (0.22), residues: 610 sheet: -0.89 (0.57), residues: 79 loop : -1.90 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.027 0.001 PHE A 101 TYR 0.015 0.001 TYR A1037 ARG 0.002 0.000 ARG A 958 *********************** 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 131 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 96 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5797 (pttm) cc_final: 0.5384 (tttp) REVERT: A 288 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5412 (t80) REVERT: A 349 ASN cc_start: 0.7475 (m-40) cc_final: 0.7018 (t0) REVERT: A 436 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6784 (m-30) REVERT: A 622 PHE cc_start: 0.6308 (t80) cc_final: 0.5679 (m-10) REVERT: A 631 MET cc_start: 0.7450 (tmm) cc_final: 0.7232 (tmm) REVERT: A 632 PHE cc_start: 0.7030 (t80) cc_final: 0.6624 (t80) REVERT: A 872 MET cc_start: 0.8034 (mmm) cc_final: 0.7654 (mmm) REVERT: A 1114 MET cc_start: 0.6822 (tmm) cc_final: 0.6134 (tmm) REVERT: A 1220 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7065 (tp) outliers start: 35 outliers final: 28 residues processed: 128 average time/residue: 0.1646 time to fit residues: 33.0298 Evaluate side-chains 120 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 89 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE 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: 0.7980 chunk 64 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7350 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9876 Z= 0.179 Angle : 0.655 9.911 13454 Z= 0.313 Chirality : 0.044 0.264 1573 Planarity : 0.004 0.054 1690 Dihedral : 7.540 55.975 1746 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 3.48 % Allowed : 21.55 % Favored : 74.98 % 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: 1.23 (0.22), residues: 609 sheet: -0.76 (0.58), residues: 79 loop : -1.84 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 583 HIS 0.007 0.001 HIS A1042 PHE 0.028 0.001 PHE A 736 TYR 0.014 0.001 TYR A 570 ARG 0.001 0.000 ARG A 116 *********************** 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 128 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5815 (pttm) cc_final: 0.5423 (tttp) REVERT: A 288 PHE cc_start: 0.6444 (OUTLIER) cc_final: 0.5373 (t80) REVERT: A 349 ASN cc_start: 0.7445 (m-40) cc_final: 0.6975 (t0) REVERT: A 436 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6727 (m-30) REVERT: A 632 PHE cc_start: 0.6955 (t80) cc_final: 0.6574 (t80) REVERT: A 872 MET cc_start: 0.8009 (mmm) cc_final: 0.7598 (mmm) REVERT: A 1114 MET cc_start: 0.6827 (tmm) cc_final: 0.6139 (tmm) REVERT: A 1220 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6998 (tp) outliers start: 36 outliers final: 27 residues processed: 124 average time/residue: 0.1584 time to fit residues: 30.9839 Evaluate side-chains 122 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 PHE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7362 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9876 Z= 0.202 Angle : 0.668 9.741 13454 Z= 0.321 Chirality : 0.044 0.269 1573 Planarity : 0.004 0.055 1690 Dihedral : 7.327 56.206 1744 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.14 % Favored : 93.69 % Rotamer: Outliers : 3.29 % Allowed : 21.84 % Favored : 74.88 % 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: -0.17 (0.25), residues: 1188 helix: 1.27 (0.22), residues: 609 sheet: -0.68 (0.59), residues: 79 loop : -1.82 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 260 HIS 0.008 0.001 HIS A1042 PHE 0.029 0.001 PHE A 736 TYR 0.015 0.001 TYR A1037 ARG 0.002 0.000 ARG A 794 ********************** 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 124 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LYS cc_start: 0.5897 (pttm) cc_final: 0.5365 (ttmm) REVERT: A 349 ASN cc_start: 0.7454 (m-40) cc_final: 0.7002 (t0) REVERT: A 436 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: A 632 PHE cc_start: 0.7114 (t80) cc_final: 0.6721 (t80) REVERT: A 872 MET cc_start: 0.7974 (mmm) cc_final: 0.7554 (mmm) REVERT: A 1114 MET cc_start: 0.6846 (tmm) cc_final: 0.6174 (tmm) REVERT: A 1220 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.7017 (tp) outliers start: 34 outliers final: 31 residues processed: 119 average time/residue: 0.1706 time to fit residues: 31.7472 Evaluate side-chains 122 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 89 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 244 SER Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 738 SER Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 857 ASP Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1043 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1158 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1220 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 87 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 94 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- 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** ** A1042 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.167003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127620 restraints weight = 13685.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127175 restraints weight = 8548.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128610 restraints weight = 8090.572| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 9876 Z= 0.333 Angle : 1.000 59.198 13454 Z= 0.542 Chirality : 0.047 0.725 1573 Planarity : 0.004 0.055 1690 Dihedral : 7.325 56.185 1744 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.23 % Favored : 93.60 % Rotamer: Outliers : 3.29 % Allowed : 21.64 % Favored : 75.07 % Cbeta Deviations : 0.09 % 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: 1.27 (0.22), residues: 609 sheet: -0.69 (0.59), residues: 79 loop : -1.81 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 260 HIS 0.013 0.001 HIS A1042 PHE 0.027 0.001 PHE A 736 TYR 0.015 0.001 TYR A1037 ARG 0.001 0.000 ARG A 958 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1808.36 seconds wall clock time: 34 minutes 3.28 seconds (2043.28 seconds total)