Starting phenix.real_space_refine on Wed Aug 5 03:22:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfp_44502/08_2026/9bfp_44502.cif" } resolution = 2.78 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 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= -0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5251 2.51 5 N 1447 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8263 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8207 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 961} Chain breaks: 5 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'TRP:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 60 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: "A" 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 Time building chain proxies: 1.86, per 1000 atoms: 0.23 Number of scatterers: 8263 At special positions: 0 Unit cell: (79.68, 86.32, 163.51, 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 34 16.00 O 1531 8.00 N 1447 7.00 C 5251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A2601 " - " ASN A 505 " " NAG A2602 " - " ASN A1228 " " NAG B 1 " - " ASN A 966 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 334.4 milliseconds 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 8.6% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.510A pdb=" N ARG A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.717A pdb=" N ARG A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 312 removed outlier: 3.823A pdb=" N ILE A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N HIS A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.878A pdb=" N ALA A1070 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.692A pdb=" N SER A1176 " --> pdb=" O ASP A1173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317 removed outlier: 3.978A pdb=" N LEU A 329 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 450 removed outlier: 5.052A pdb=" N ILE A 443 " --> pdb=" O HIS A 459 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N HIS A 459 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 488 removed outlier: 3.570A pdb=" N GLY A 524 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568 removed outlier: 7.014A pdb=" N VAL A 552 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 810 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 573 through 576 removed outlier: 7.026A pdb=" N LEU A 588 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LYS A 598 " --> pdb=" O PRO A 607 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLU A 600 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 605 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 631 removed outlier: 6.577A pdb=" N ALA A 640 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 628 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR A 638 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 630 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 636 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 652 " --> pdb=" O MET A 641 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 624 through 631 removed outlier: 6.577A pdb=" N ALA A 640 " --> pdb=" O ARG A 626 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU A 628 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR A 638 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N PHE A 630 " --> pdb=" O ARG A 636 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG A 636 " --> pdb=" O PHE A 630 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE A 654 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 676 through 680 removed outlier: 3.746A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A 688 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 694 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.528A pdb=" N ILE A 724 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 770 through 772 removed outlier: 3.753A pdb=" N ALA A 798 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 832 through 835 Processing sheet with id=AB5, first strand: chain 'A' and resid 875 through 881 removed outlier: 5.852A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 949 through 954 removed outlier: 5.284A pdb=" N VAL A 938 " --> pdb=" O GLN A 951 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 939 " --> pdb=" O TRP A 931 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A1180 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 963 through 964 removed outlier: 3.530A pdb=" N TYR A 972 " --> pdb=" O HIS A 980 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.773A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A1022 " --> pdb=" O LEU A1035 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 6.581A pdb=" N LEU A1060 " --> pdb=" O TYR A1073 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1081 through 1089 removed outlier: 6.607A pdb=" N LEU A1098 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE A1086 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N PHE A1096 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU A1088 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLN A1094 " --> pdb=" O LEU A1088 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP A1097 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A1104 " --> pdb=" O GLY A1101 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A1105 " --> pdb=" O GLN A1124 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A1124 " --> pdb=" O LEU A1105 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A1107 " --> pdb=" O ILE A1122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1137 through 1139 Processing sheet with id=AC3, first strand: chain 'A' and resid 1207 through 1209 removed outlier: 4.513A pdb=" N HIS A1217 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL A1218 " --> pdb=" O ALA A1253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1243 through 1248 279 hydrogen bonds defined for protein. 714 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: 1.39 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2631 1.34 - 1.46: 2043 1.46 - 1.59: 3756 1.59 - 1.72: 0 1.72 - 1.84: 52 Bond restraints: 8482 Sorted by residual: bond pdb=" N ASN A 905 " pdb=" CA ASN A 905 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.27e-02 6.20e+03 8.30e+00 bond pdb=" N VAL A 420 " pdb=" CA VAL A 420 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.27e-02 6.20e+03 7.53e+00 bond pdb=" N VAL A 906 " pdb=" CA VAL A 906 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.21e+00 bond pdb=" CA SER A 862 " pdb=" CB SER A 862 " ideal model delta sigma weight residual 1.530 1.490 0.041 1.52e-02 4.33e+03 7.16e+00 bond pdb=" CA SER A 860 " pdb=" CB SER A 860 " ideal model delta sigma weight residual 1.528 1.492 0.036 1.35e-02 5.49e+03 6.97e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 11242 3.38 - 6.77: 255 6.77 - 10.15: 40 10.15 - 13.53: 8 13.53 - 16.92: 1 Bond angle restraints: 11546 Sorted by residual: angle pdb=" C PHE A 413 " pdb=" CA PHE A 413 " pdb=" CB PHE A 413 " ideal model delta sigma weight residual 110.85 119.75 -8.90 1.70e+00 3.46e-01 2.74e+01 angle pdb=" C SER A 823 " pdb=" N ALA A 824 " pdb=" CA ALA A 824 " ideal model delta sigma weight residual 123.05 130.89 -7.84 1.57e+00 4.06e-01 2.49e+01 angle pdb=" C ASN A 690 " pdb=" N GLU A 691 " pdb=" CA GLU A 691 " ideal model delta sigma weight residual 120.28 127.34 -7.06 1.44e+00 4.82e-01 2.40e+01 angle pdb=" OG1 THR A1273 " pdb=" CB THR A1273 " pdb=" CG2 THR A1273 " ideal model delta sigma weight residual 109.30 99.59 9.71 2.00e+00 2.50e-01 2.36e+01 angle pdb=" C THR A 464 " pdb=" N ASN A 465 " pdb=" CA ASN A 465 " ideal model delta sigma weight residual 122.19 129.03 -6.84 1.41e+00 5.03e-01 2.36e+01 ... (remaining 11541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4721 17.97 - 35.93: 332 35.93 - 53.90: 59 53.90 - 71.87: 15 71.87 - 89.83: 8 Dihedral angle restraints: 5135 sinusoidal: 2150 harmonic: 2985 Sorted by residual: dihedral pdb=" CB CYS A 981 " pdb=" SG CYS A 981 " pdb=" SG CYS A 991 " pdb=" CB CYS A 991 " ideal model delta sinusoidal sigma weight residual 93.00 139.96 -46.96 1 1.00e+01 1.00e-02 3.05e+01 dihedral pdb=" CA SER A1176 " pdb=" C SER A1176 " pdb=" N PRO A1177 " pdb=" CA PRO A1177 " ideal model delta harmonic sigma weight residual 180.00 153.74 26.26 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN A 505 " pdb=" C ASN A 505 " pdb=" N TYR A 506 " pdb=" CA TYR A 506 " ideal model delta harmonic sigma weight residual 180.00 -154.04 -25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1046 0.082 - 0.164: 176 0.164 - 0.246: 17 0.246 - 0.329: 8 0.329 - 0.411: 3 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB VAL A 526 " pdb=" CA VAL A 526 " pdb=" CG1 VAL A 526 " pdb=" CG2 VAL A 526 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB ILE A 686 " pdb=" CA ILE A 686 " pdb=" CG1 ILE A 686 " pdb=" CG2 ILE A 686 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CB ILE A 982 " pdb=" CA ILE A 982 " pdb=" CG1 ILE A 982 " pdb=" CG2 ILE A 982 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 1247 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 336 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C HIS A 336 " 0.068 2.00e-02 2.50e+03 pdb=" O HIS A 336 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE A 337 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 966 " 0.035 2.00e-02 2.50e+03 3.38e-02 1.43e+01 pdb=" CG ASN A 966 " -0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN A 966 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 966 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 347 " 0.018 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE A 347 " -0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 347 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 347 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 347 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 347 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 347 " -0.001 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2664 2.86 - 3.37: 6039 3.37 - 3.88: 13927 3.88 - 4.39: 15143 4.39 - 4.90: 26946 Nonbonded interactions: 64719 Sorted by model distance: nonbonded pdb=" O LYS A 250 " pdb=" OG1 THR A 254 " model vdw 2.356 3.040 nonbonded pdb=" OG SER A1225 " pdb=" O GLY A1227 " model vdw 2.377 3.040 nonbonded pdb=" OG SER A 933 " pdb=" OG SER A 937 " model vdw 2.384 3.040 nonbonded pdb=" OE1 GLN A 352 " pdb=" NH2 ARG A 406 " model vdw 2.414 3.120 nonbonded pdb=" N SER A 862 " pdb=" O SER A 862 " model vdw 2.433 2.496 ... (remaining 64714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 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 : 0.007 0.062 8493 Z= 0.336 Angle : 1.241 16.916 11572 Z= 0.668 Chirality : 0.066 0.411 1250 Planarity : 0.010 0.089 1506 Dihedral : 13.561 89.833 3190 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.24), residues: 1022 helix: -3.73 (0.32), residues: 73 sheet: -0.52 (0.24), residues: 438 loop : -1.74 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 882 TYR 0.036 0.003 TYR A 740 PHE 0.063 0.004 PHE A 347 TRP 0.056 0.003 TRP A 333 HIS 0.013 0.002 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.34 ( 8482) covalent geometry : angle 1.23463 / 0.67 (11546) SS BOND : bond 0.00385 / 0.25 ( 7) SS BOND : angle 2.77125 / 1.75 ( 14) hydrogen bonds : bond 0.21333 / 14.62 ( 268) hydrogen bonds : angle 9.21658 / 6.31 ( 714) link_BETA1-4 : bond 0.00261 / 0.16 ( 1) link_BETA1-4 : angle 3.92897 / 1.95 ( 3) link_NAG-ASN : bond 0.01567 / 0.89 ( 3) link_NAG-ASN : angle 2.72395 / 1.36 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8040 (pt0) cc_final: 0.7826 (pt0) REVERT: A 265 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8087 (mtmt) REVERT: A 462 ARG cc_start: 0.7817 (ttt90) cc_final: 0.7103 (tmt-80) REVERT: A 507 THR cc_start: 0.7964 (m) cc_final: 0.7730 (p) REVERT: A 600 GLU cc_start: 0.8148 (pp20) cc_final: 0.7894 (pm20) REVERT: A 859 ARG cc_start: 0.7651 (mmm160) cc_final: 0.7126 (mmp-170) REVERT: A 868 LEU cc_start: 0.8479 (tp) cc_final: 0.8261 (OUTLIER) REVERT: A 889 GLN cc_start: 0.8637 (mt0) cc_final: 0.8271 (mm-40) REVERT: A 935 GLN cc_start: 0.7713 (tm-30) cc_final: 0.7406 (pm20) REVERT: A 978 LEU cc_start: 0.8266 (mt) cc_final: 0.8043 (mm) REVERT: A 1120 GLN cc_start: 0.7055 (mp10) cc_final: 0.6689 (mp10) REVERT: A 1150 ARG cc_start: 0.8232 (ttm110) cc_final: 0.7978 (ttp80) REVERT: A 1199 MET cc_start: 0.8025 (ptm) cc_final: 0.7410 (mmm) REVERT: A 1239 PHE cc_start: 0.8163 (p90) cc_final: 0.7889 (p90) outliers start: 0 outliers final: 2 residues processed: 157 average time/residue: 0.4664 time to fit residues: 77.4774 Evaluate side-chains 98 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 501 GLN A 563 ASN A1124 GLN A1174 GLN A1264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.105967 restraints weight = 10231.227| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.69 r_work: 0.3108 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8493 Z= 0.156 Angle : 0.623 6.699 11572 Z= 0.316 Chirality : 0.043 0.158 1250 Planarity : 0.006 0.049 1506 Dihedral : 5.420 27.762 1216 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.05 % Allowed : 8.67 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1022 helix: -0.95 (0.54), residues: 76 sheet: -0.39 (0.25), residues: 444 loop : -1.15 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 550 TYR 0.017 0.001 TYR A 740 PHE 0.018 0.002 PHE A 651 TRP 0.021 0.002 TRP A 333 HIS 0.004 0.001 HIS A 927 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 8482) covalent geometry : angle 0.61798 / 0.32 (11546) SS BOND : bond 0.00270 / 0.19 ( 7) SS BOND : angle 0.94232 / 0.63 ( 14) hydrogen bonds : bond 0.04014 / 2.78 ( 268) hydrogen bonds : angle 6.31851 / 4.22 ( 714) link_BETA1-4 : bond 0.01071 / 0.67 ( 1) link_BETA1-4 : angle 3.07642 / 1.52 ( 3) link_NAG-ASN : bond 0.00875 / 0.45 ( 3) link_NAG-ASN : angle 2.11169 / 0.97 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8142 (mtpt) cc_final: 0.7745 (mtmt) REVERT: A 462 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7091 (tmt-80) REVERT: A 603 GLN cc_start: 0.8350 (mm110) cc_final: 0.8018 (mm110) REVERT: A 719 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7979 (mm-40) REVERT: A 882 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8142 (mmp80) REVERT: A 1150 ARG cc_start: 0.8226 (ttm110) cc_final: 0.8017 (ttp80) REVERT: A 1167 MET cc_start: 0.8154 (mtp) cc_final: 0.7541 (mtm) REVERT: A 1199 MET cc_start: 0.8042 (ptm) cc_final: 0.7748 (mmm) outliers start: 18 outliers final: 2 residues processed: 104 average time/residue: 0.4519 time to fit residues: 50.1121 Evaluate side-chains 81 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 78 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 719 GLN Chi-restraints excluded: chain A residue 1090 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 32 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104943 restraints weight = 10186.892| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.72 r_work: 0.3091 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8493 Z= 0.124 Angle : 0.561 6.235 11572 Z= 0.279 Chirality : 0.042 0.159 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.780 25.784 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.94 % Allowed : 12.54 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.26), residues: 1022 helix: 0.72 (0.64), residues: 72 sheet: -0.38 (0.24), residues: 459 loop : -0.56 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 492 TYR 0.013 0.001 TYR A 740 PHE 0.014 0.001 PHE A 651 TRP 0.018 0.001 TRP A 333 HIS 0.005 0.001 HIS A 986 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8482) covalent geometry : angle 0.55670 / 0.28 (11546) SS BOND : bond 0.00191 / 0.13 ( 7) SS BOND : angle 0.68554 / 0.45 ( 14) hydrogen bonds : bond 0.03321 / 2.29 ( 268) hydrogen bonds : angle 5.66440 / 3.79 ( 714) link_BETA1-4 : bond 0.00739 / 0.46 ( 1) link_BETA1-4 : angle 2.06021 / 1.02 ( 3) link_NAG-ASN : bond 0.00567 / 0.29 ( 3) link_NAG-ASN : angle 2.36253 / 1.11 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7647 (mtmt) REVERT: A 462 ARG cc_start: 0.7820 (ttt90) cc_final: 0.7143 (ttt-90) REVERT: A 550 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8169 (tpp-160) REVERT: A 553 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8083 (mmm) REVERT: A 565 MET cc_start: 0.8722 (tpp) cc_final: 0.8418 (tpp) REVERT: A 603 GLN cc_start: 0.8373 (mm110) cc_final: 0.8096 (mm110) REVERT: A 1150 ARG cc_start: 0.8247 (ttm110) cc_final: 0.8017 (ttp80) REVERT: A 1167 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: A 1243 LEU cc_start: 0.8754 (mp) cc_final: 0.8511 (mt) outliers start: 17 outliers final: 3 residues processed: 105 average time/residue: 0.4496 time to fit residues: 50.7017 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN A 278 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.137459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100875 restraints weight = 10396.281| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.69 r_work: 0.3092 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8493 Z= 0.146 Angle : 0.560 6.414 11572 Z= 0.276 Chirality : 0.042 0.143 1250 Planarity : 0.004 0.037 1506 Dihedral : 4.685 25.957 1214 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.05 % Allowed : 13.45 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 1022 helix: 1.25 (0.66), residues: 72 sheet: -0.31 (0.25), residues: 458 loop : -0.35 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.019 0.001 TYR A 567 PHE 0.013 0.001 PHE A 735 TRP 0.016 0.001 TRP A 623 HIS 0.007 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 8482) covalent geometry : angle 0.55201 / 0.27 (11546) SS BOND : bond 0.00228 / 0.16 ( 7) SS BOND : angle 0.61619 / 0.38 ( 14) hydrogen bonds : bond 0.03055 / 2.09 ( 268) hydrogen bonds : angle 5.47511 / 3.66 ( 714) link_BETA1-4 : bond 0.00871 / 0.54 ( 1) link_BETA1-4 : angle 1.90430 / 0.98 ( 3) link_NAG-ASN : bond 0.00613 / 0.31 ( 3) link_NAG-ASN : angle 3.22645 / 1.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8077 (mtpt) cc_final: 0.7617 (mtmt) REVERT: A 266 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: A 384 ASP cc_start: 0.8188 (t70) cc_final: 0.7977 (t0) REVERT: A 462 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7462 (ttt-90) REVERT: A 550 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8378 (tpp-160) REVERT: A 603 GLN cc_start: 0.8460 (mm110) cc_final: 0.8216 (mm110) REVERT: A 1150 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8164 (ttp80) REVERT: A 1167 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7732 (mtm) REVERT: A 1243 LEU cc_start: 0.8801 (mp) cc_final: 0.8595 (mt) outliers start: 18 outliers final: 5 residues processed: 94 average time/residue: 0.5030 time to fit residues: 50.9913 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 88 optimal weight: 0.0980 chunk 83 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 73 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.3233 > 50:) chunk 4 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 93 optimal weight: 0.0170 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 HIS A 951 GLN A1174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.138327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102068 restraints weight = 10322.886| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.68 r_work: 0.3119 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8493 Z= 0.103 Angle : 0.527 8.392 11572 Z= 0.261 Chirality : 0.041 0.143 1250 Planarity : 0.004 0.038 1506 Dihedral : 4.372 24.451 1214 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.60 % Allowed : 14.71 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.26), residues: 1022 helix: 1.64 (0.66), residues: 72 sheet: -0.25 (0.25), residues: 458 loop : -0.18 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.019 0.001 TYR A 567 PHE 0.011 0.001 PHE A 735 TRP 0.019 0.001 TRP A 989 HIS 0.006 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.10 ( 8482) covalent geometry : angle 0.52235 / 0.26 (11546) SS BOND : bond 0.00213 / 0.14 ( 7) SS BOND : angle 0.49623 / 0.30 ( 14) hydrogen bonds : bond 0.02759 / 1.89 ( 268) hydrogen bonds : angle 5.24030 / 3.48 ( 714) link_BETA1-4 : bond 0.00734 / 0.46 ( 1) link_BETA1-4 : angle 1.58395 / 0.84 ( 3) link_NAG-ASN : bond 0.00322 / 0.17 ( 3) link_NAG-ASN : angle 2.53276 / 1.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7579 (mtmt) REVERT: A 384 ASP cc_start: 0.8169 (t70) cc_final: 0.7963 (t0) REVERT: A 462 ARG cc_start: 0.7954 (ttt90) cc_final: 0.7397 (ttt-90) REVERT: A 603 GLN cc_start: 0.8507 (mm110) cc_final: 0.8242 (mm110) REVERT: A 1150 ARG cc_start: 0.8358 (ttm110) cc_final: 0.8147 (ttp80) REVERT: A 1167 MET cc_start: 0.8328 (mtp) cc_final: 0.7741 (mtm) outliers start: 14 outliers final: 6 residues processed: 103 average time/residue: 0.5027 time to fit residues: 55.7736 Evaluate side-chains 85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 47 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 0.0050 chunk 5 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN A 951 GLN A1174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100812 restraints weight = 10210.549| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.69 r_work: 0.3092 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8493 Z= 0.120 Angle : 0.534 7.357 11572 Z= 0.263 Chirality : 0.042 0.157 1250 Planarity : 0.004 0.038 1506 Dihedral : 4.283 22.949 1214 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.05 % Allowed : 15.85 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.27), residues: 1022 helix: 1.84 (0.65), residues: 72 sheet: -0.11 (0.26), residues: 437 loop : -0.06 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 406 TYR 0.020 0.001 TYR A 567 PHE 0.011 0.001 PHE A 735 TRP 0.021 0.001 TRP A 989 HIS 0.006 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8482) covalent geometry : angle 0.53005 / 0.26 (11546) SS BOND : bond 0.00208 / 0.14 ( 7) SS BOND : angle 0.58304 / 0.35 ( 14) hydrogen bonds : bond 0.02769 / 1.88 ( 268) hydrogen bonds : angle 5.19840 / 3.45 ( 714) link_BETA1-4 : bond 0.00718 / 0.45 ( 1) link_BETA1-4 : angle 1.36577 / 0.70 ( 3) link_NAG-ASN : bond 0.00268 / 0.14 ( 3) link_NAG-ASN : angle 2.28620 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8541 (t0) cc_final: 0.8233 (t0) REVERT: A 265 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7577 (mtmt) REVERT: A 266 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: A 384 ASP cc_start: 0.8283 (t70) cc_final: 0.8033 (t0) REVERT: A 462 ARG cc_start: 0.7953 (ttt90) cc_final: 0.7531 (ttt-90) REVERT: A 550 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8442 (tpp-160) REVERT: A 603 GLN cc_start: 0.8500 (mm110) cc_final: 0.8149 (mm110) REVERT: A 1150 ARG cc_start: 0.8389 (ttm110) cc_final: 0.8173 (ttp80) REVERT: A 1167 MET cc_start: 0.8355 (mtp) cc_final: 0.7747 (mtm) outliers start: 18 outliers final: 5 residues processed: 97 average time/residue: 0.5243 time to fit residues: 54.6325 Evaluate side-chains 83 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 16 optimal weight: 0.0970 chunk 100 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.113373 restraints weight = 10810.694| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.59 r_work: 0.3292 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8493 Z= 0.109 Angle : 0.527 6.407 11572 Z= 0.262 Chirality : 0.042 0.161 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.194 22.157 1214 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.28 % Allowed : 16.19 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.27), residues: 1022 helix: 2.05 (0.64), residues: 72 sheet: -0.09 (0.26), residues: 437 loop : -0.01 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 879 TYR 0.019 0.001 TYR A 567 PHE 0.011 0.001 PHE A 735 TRP 0.020 0.001 TRP A 989 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 8482) covalent geometry : angle 0.52285 / 0.26 (11546) SS BOND : bond 0.00208 / 0.14 ( 7) SS BOND : angle 0.57674 / 0.35 ( 14) hydrogen bonds : bond 0.02680 / 1.82 ( 268) hydrogen bonds : angle 5.15613 / 3.42 ( 714) link_BETA1-4 : bond 0.00564 / 0.35 ( 1) link_BETA1-4 : angle 1.32810 / 0.70 ( 3) link_NAG-ASN : bond 0.00199 / 0.10 ( 3) link_NAG-ASN : angle 2.19454 / 1.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8560 (t0) cc_final: 0.8285 (t0) REVERT: A 265 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7424 (mtmt) REVERT: A 266 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 384 ASP cc_start: 0.8312 (t70) cc_final: 0.8032 (t0) REVERT: A 462 ARG cc_start: 0.7882 (ttt90) cc_final: 0.7430 (ttt-90) REVERT: A 527 GLN cc_start: 0.8231 (pt0) cc_final: 0.7937 (pm20) REVERT: A 549 ARG cc_start: 0.8553 (mmp80) cc_final: 0.8283 (mmp80) REVERT: A 550 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8398 (tpp-160) REVERT: A 565 MET cc_start: 0.9184 (tpp) cc_final: 0.8978 (tpp) REVERT: A 603 GLN cc_start: 0.8436 (mm110) cc_final: 0.8088 (mm110) REVERT: A 907 ASP cc_start: 0.8700 (m-30) cc_final: 0.8491 (m-30) REVERT: A 1150 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8161 (ttp80) REVERT: A 1167 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7642 (mtm) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 0.4928 time to fit residues: 48.6848 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 0.0980 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** A1174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113237 restraints weight = 10780.046| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.60 r_work: 0.3287 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8493 Z= 0.111 Angle : 0.530 6.699 11572 Z= 0.260 Chirality : 0.042 0.136 1250 Planarity : 0.004 0.042 1506 Dihedral : 4.223 21.087 1214 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.71 % Allowed : 17.22 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 1022 helix: 2.13 (0.64), residues: 72 sheet: -0.07 (0.26), residues: 439 loop : 0.02 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 879 TYR 0.018 0.001 TYR A 567 PHE 0.011 0.001 PHE A 735 TRP 0.020 0.001 TRP A 989 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 8482) covalent geometry : angle 0.52091 / 0.26 (11546) SS BOND : bond 0.00210 / 0.14 ( 7) SS BOND : angle 0.60587 / 0.37 ( 14) hydrogen bonds : bond 0.02652 / 1.80 ( 268) hydrogen bonds : angle 5.12372 / 3.39 ( 714) link_BETA1-4 : bond 0.00646 / 0.40 ( 1) link_BETA1-4 : angle 1.30905 / 0.69 ( 3) link_NAG-ASN : bond 0.00167 / 0.08 ( 3) link_NAG-ASN : angle 3.54629 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8547 (t0) cc_final: 0.8235 (t0) REVERT: A 234 GLU cc_start: 0.8136 (pt0) cc_final: 0.7693 (pt0) REVERT: A 265 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7397 (mtmt) REVERT: A 266 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 384 ASP cc_start: 0.8306 (t70) cc_final: 0.8011 (t0) REVERT: A 462 ARG cc_start: 0.7884 (ttt90) cc_final: 0.7421 (ttt-90) REVERT: A 527 GLN cc_start: 0.8237 (pt0) cc_final: 0.7931 (pm20) REVERT: A 550 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8405 (tpp-160) REVERT: A 603 GLN cc_start: 0.8427 (mm110) cc_final: 0.8079 (mm110) REVERT: A 1150 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8159 (ttp80) REVERT: A 1167 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7627 (mtm) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 0.5386 time to fit residues: 50.9438 Evaluate side-chains 85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.0770 chunk 83 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.144263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113851 restraints weight = 10796.939| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.48 r_work: 0.3289 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8493 Z= 0.122 Angle : 0.538 6.974 11572 Z= 0.265 Chirality : 0.042 0.136 1250 Planarity : 0.004 0.042 1506 Dihedral : 4.226 19.565 1214 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 17.22 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 1022 helix: 2.17 (0.64), residues: 72 sheet: -0.07 (0.26), residues: 439 loop : 0.03 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 549 TYR 0.017 0.001 TYR A 567 PHE 0.010 0.001 PHE A 735 TRP 0.022 0.001 TRP A 989 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8482) covalent geometry : angle 0.53155 / 0.26 (11546) SS BOND : bond 0.00215 / 0.14 ( 7) SS BOND : angle 0.64812 / 0.40 ( 14) hydrogen bonds : bond 0.02672 / 1.81 ( 268) hydrogen bonds : angle 5.11431 / 3.38 ( 714) link_BETA1-4 : bond 0.00729 / 0.46 ( 1) link_BETA1-4 : angle 1.10271 / 0.58 ( 3) link_NAG-ASN : bond 0.00230 / 0.12 ( 3) link_NAG-ASN : angle 2.86078 / 1.43 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8528 (t0) cc_final: 0.8239 (t0) REVERT: A 234 GLU cc_start: 0.8116 (pt0) cc_final: 0.7688 (pt0) REVERT: A 265 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7446 (mtmt) REVERT: A 266 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 384 ASP cc_start: 0.8341 (t70) cc_final: 0.8034 (t70) REVERT: A 462 ARG cc_start: 0.7873 (ttt90) cc_final: 0.7425 (ttt-90) REVERT: A 527 GLN cc_start: 0.8282 (pt0) cc_final: 0.7950 (pm20) REVERT: A 550 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8390 (tpp-160) REVERT: A 603 GLN cc_start: 0.8440 (mm110) cc_final: 0.8106 (mm110) REVERT: A 882 ARG cc_start: 0.8787 (mmp80) cc_final: 0.8525 (mmm160) REVERT: A 1150 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8169 (ttp80) REVERT: A 1167 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7668 (mtm) outliers start: 16 outliers final: 9 residues processed: 89 average time/residue: 0.5517 time to fit residues: 52.8511 Evaluate side-chains 86 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 34 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 0.0010 chunk 54 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 100 optimal weight: 0.0470 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 0.7980 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.110665 restraints weight = 10709.870| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.66 r_work: 0.3281 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8493 Z= 0.102 Angle : 0.534 11.376 11572 Z= 0.265 Chirality : 0.041 0.143 1250 Planarity : 0.004 0.043 1506 Dihedral : 4.194 18.871 1214 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.25 % Allowed : 17.90 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 1022 helix: 2.31 (0.63), residues: 72 sheet: -0.02 (0.26), residues: 443 loop : 0.06 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 879 TYR 0.018 0.001 TYR A 567 PHE 0.011 0.001 PHE A 735 TRP 0.027 0.001 TRP A 989 HIS 0.005 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 8482) covalent geometry : angle 0.52852 / 0.26 (11546) SS BOND : bond 0.00206 / 0.13 ( 7) SS BOND : angle 0.60666 / 0.37 ( 14) hydrogen bonds : bond 0.02607 / 1.77 ( 268) hydrogen bonds : angle 5.05573 / 3.34 ( 714) link_BETA1-4 : bond 0.00545 / 0.34 ( 1) link_BETA1-4 : angle 1.26408 / 0.66 ( 3) link_NAG-ASN : bond 0.00149 / 0.07 ( 3) link_NAG-ASN : angle 2.65599 / 1.31 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2044 Ramachandran restraints generated. 1022 Oldfield, 0 Emsley, 1022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8472 (t0) cc_final: 0.8206 (t0) REVERT: A 234 GLU cc_start: 0.8016 (pt0) cc_final: 0.7602 (pt0) REVERT: A 265 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7308 (mtmt) REVERT: A 384 ASP cc_start: 0.8328 (t70) cc_final: 0.7987 (t70) REVERT: A 462 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7235 (ttt-90) REVERT: A 527 GLN cc_start: 0.8174 (pt0) cc_final: 0.7814 (pm20) REVERT: A 550 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8397 (tpp-160) REVERT: A 603 GLN cc_start: 0.8400 (mm110) cc_final: 0.8058 (mm110) REVERT: A 710 ILE cc_start: 0.8838 (tt) cc_final: 0.8533 (tp) REVERT: A 850 ASN cc_start: 0.8027 (m-40) cc_final: 0.7801 (m-40) REVERT: A 882 ARG cc_start: 0.8707 (mmp80) cc_final: 0.8454 (mmm160) REVERT: A 978 LEU cc_start: 0.8882 (mt) cc_final: 0.8604 (mm) REVERT: A 1150 ARG cc_start: 0.8338 (ttm110) cc_final: 0.8116 (ttp80) REVERT: A 1167 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7509 (mtm) outliers start: 11 outliers final: 8 residues processed: 85 average time/residue: 0.5254 time to fit residues: 48.0094 Evaluate side-chains 87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.142141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107795 restraints weight = 10819.781| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.72 r_work: 0.3240 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8493 Z= 0.164 Angle : 0.570 10.249 11572 Z= 0.283 Chirality : 0.043 0.146 1250 Planarity : 0.004 0.042 1506 Dihedral : 4.287 18.966 1214 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.71 % Allowed : 17.56 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.27), residues: 1022 helix: 2.22 (0.63), residues: 72 sheet: 0.00 (0.26), residues: 440 loop : 0.01 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 879 TYR 0.018 0.001 TYR A 567 PHE 0.012 0.001 PHE A 716 TRP 0.030 0.001 TRP A 989 HIS 0.010 0.001 HIS A 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 ( 8482) covalent geometry : angle 0.56548 / 0.28 (11546) SS BOND : bond 0.00231 / 0.16 ( 7) SS BOND : angle 0.76171 / 0.49 ( 14) hydrogen bonds : bond 0.02807 / 1.90 ( 268) hydrogen bonds : angle 5.15699 / 3.41 ( 714) link_BETA1-4 : bond 0.00722 / 0.45 ( 1) link_BETA1-4 : angle 1.15163 / 0.57 ( 3) link_NAG-ASN : bond 0.00170 / 0.09 ( 3) link_NAG-ASN : angle 2.51771 / 1.22 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2991.70 seconds wall clock time: 51 minutes 39.23 seconds (3099.23 seconds total)