Starting phenix.real_space_refine on Tue Apr 29 05:28:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfp_44502/04_2025/9bfp_44502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfp_44502/04_2025/9bfp_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_44502/04_2025/9bfp_44502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfp_44502/04_2025/9bfp_44502.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfp_44502/04_2025/9bfp_44502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfp_44502/04_2025/9bfp_44502.cif" } resolution = 2.78 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= -0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} 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: 5.49, per 1000 atoms: 0.66 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: 1.89 Conformation dependent library (CDL) restraints added in 923.8 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: 1.39 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: 3.45 Time building geometry restraints manager: 2.27 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: 3.430 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.650 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 : 2.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (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 TRP 0.056 0.003 TRP A 333 HIS 0.013 0.002 HIS A 459 PHE 0.063 0.004 PHE A 347 TYR 0.036 0.003 TYR A 740 ARG 0.017 0.001 ARG A 882 Details of bonding type rmsd link_NAG-ASN : bond 0.01567 ( 3) link_NAG-ASN : angle 2.72395 ( 9) link_BETA1-4 : bond 0.00261 ( 1) link_BETA1-4 : angle 3.92897 ( 3) hydrogen bonds : bond 0.21333 ( 268) hydrogen bonds : angle 9.21658 ( 714) SS BOND : bond 0.00385 ( 7) SS BOND : angle 2.77125 ( 14) covalent geometry : bond 0.00677 ( 8482) covalent geometry : angle 1.23463 (11546) *********************** 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 : 0.844 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: 0.7650 (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: 1.3281 time to fit residues: 220.8611 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 : 0.967 ------------------------------------------------------------------------------- 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 86 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 93 optimal weight: 0.0470 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN A 501 GLN A1124 GLN A1174 GLN A1264 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.140558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106949 restraints weight = 10122.196| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.65 r_work: 0.3129 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1925 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= 0.141 Angle : 0.620 6.637 11572 Z= 0.313 Chirality : 0.043 0.156 1250 Planarity : 0.006 0.049 1506 Dihedral : 5.400 27.637 1216 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.94 % Allowed : 8.44 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.25), residues: 1022 helix: -0.96 (0.54), residues: 76 sheet: -0.38 (0.25), residues: 444 loop : -1.17 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 333 HIS 0.004 0.001 HIS A 927 PHE 0.018 0.002 PHE A 651 TYR 0.016 0.001 TYR A 740 ARG 0.008 0.001 ARG A 550 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 3) link_NAG-ASN : angle 2.13856 ( 9) link_BETA1-4 : bond 0.01069 ( 1) link_BETA1-4 : angle 3.09897 ( 3) hydrogen bonds : bond 0.04105 ( 268) hydrogen bonds : angle 6.33239 ( 714) SS BOND : bond 0.00253 ( 7) SS BOND : angle 0.92329 ( 14) covalent geometry : bond 0.00320 ( 8482) covalent geometry : angle 0.61541 (11546) *********************** 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 114 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7797 (mtmt) REVERT: A 462 ARG cc_start: 0.7781 (ttt90) cc_final: 0.7089 (tmt-80) REVERT: A 603 GLN cc_start: 0.8335 (mm110) cc_final: 0.8010 (mm110) REVERT: A 719 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7954 (mm-40) REVERT: A 882 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8129 (mmp80) REVERT: A 1120 GLN cc_start: 0.7277 (mp10) cc_final: 0.6885 (mp10) REVERT: A 1150 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7997 (ttp80) REVERT: A 1167 MET cc_start: 0.8175 (mtp) cc_final: 0.7568 (mtm) REVERT: A 1199 MET cc_start: 0.8030 (ptm) cc_final: 0.7771 (mmm) outliers start: 17 outliers final: 2 residues processed: 106 average time/residue: 1.3046 time to fit residues: 147.0656 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 71 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 940 HIS ** A 986 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 GLN A1174 GLN A1229 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109875 restraints weight = 10883.705| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.53 r_work: 0.3230 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8493 Z= 0.227 Angle : 0.644 7.122 11572 Z= 0.319 Chirality : 0.045 0.141 1250 Planarity : 0.005 0.041 1506 Dihedral : 5.172 28.957 1214 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.74 % Allowed : 12.09 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1022 helix: 0.53 (0.66), residues: 72 sheet: -0.37 (0.24), residues: 453 loop : -0.60 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 333 HIS 0.004 0.001 HIS A 986 PHE 0.018 0.002 PHE A 413 TYR 0.025 0.002 TYR A 740 ARG 0.007 0.001 ARG A 492 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 2.52936 ( 9) link_BETA1-4 : bond 0.00953 ( 1) link_BETA1-4 : angle 1.67566 ( 3) hydrogen bonds : bond 0.03845 ( 268) hydrogen bonds : angle 5.79433 ( 714) SS BOND : bond 0.00277 ( 7) SS BOND : angle 0.89839 ( 14) covalent geometry : bond 0.00529 ( 8482) covalent geometry : angle 0.63957 (11546) *********************** 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 115 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7569 (mtmt) REVERT: A 266 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: A 384 ASP cc_start: 0.8227 (t70) cc_final: 0.7986 (t0) REVERT: A 462 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7185 (ttt-90) REVERT: A 600 GLU cc_start: 0.8333 (pp20) cc_final: 0.8035 (pp20) REVERT: A 603 GLN cc_start: 0.8417 (mm110) cc_final: 0.8170 (mm110) REVERT: A 665 LYS cc_start: 0.8227 (mtmt) cc_final: 0.7976 (mtmt) REVERT: A 710 ILE cc_start: 0.9013 (tt) cc_final: 0.8735 (tt) REVERT: A 859 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7004 (mmp-170) REVERT: A 1126 LYS cc_start: 0.8512 (mmtt) cc_final: 0.7755 (mppt) REVERT: A 1150 ARG cc_start: 0.8408 (ttm110) cc_final: 0.8194 (ttp80) REVERT: A 1167 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7636 (mtm) REVERT: A 1199 MET cc_start: 0.8132 (ptm) cc_final: 0.7718 (mmm) REVERT: A 1243 LEU cc_start: 0.8818 (mp) cc_final: 0.8576 (mt) outliers start: 24 outliers final: 5 residues processed: 105 average time/residue: 1.1736 time to fit residues: 131.6993 Evaluate side-chains 85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 1090 THR 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 37 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 278 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 ASN A 568 GLN A1174 GLN A1229 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.142233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110667 restraints weight = 10767.781| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.51 r_work: 0.3248 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8493 Z= 0.162 Angle : 0.574 6.623 11572 Z= 0.284 Chirality : 0.042 0.139 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.892 29.536 1214 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.17 % Allowed : 13.45 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.26), residues: 1022 helix: 0.95 (0.66), residues: 72 sheet: -0.34 (0.24), residues: 458 loop : -0.40 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE A 735 TYR 0.010 0.001 TYR A 740 ARG 0.004 0.000 ARG A 492 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 3) link_NAG-ASN : angle 3.23074 ( 9) link_BETA1-4 : bond 0.01085 ( 1) link_BETA1-4 : angle 1.82121 ( 3) hydrogen bonds : bond 0.03184 ( 268) hydrogen bonds : angle 5.58926 ( 714) SS BOND : bond 0.00254 ( 7) SS BOND : angle 0.65232 ( 14) covalent geometry : bond 0.00374 ( 8482) covalent geometry : angle 0.56661 (11546) *********************** 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 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7544 (mtmt) REVERT: A 384 ASP cc_start: 0.8252 (t70) cc_final: 0.8018 (t0) REVERT: A 462 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7217 (ttt-90) REVERT: A 553 MET cc_start: 0.8751 (mmm) cc_final: 0.8174 (mmm) REVERT: A 565 MET cc_start: 0.9054 (tpp) cc_final: 0.8644 (tpp) REVERT: A 600 GLU cc_start: 0.8322 (pp20) cc_final: 0.8009 (pp20) REVERT: A 603 GLN cc_start: 0.8460 (mm110) cc_final: 0.8190 (mm110) REVERT: A 665 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7973 (mtmt) REVERT: A 704 ILE cc_start: 0.8385 (mp) cc_final: 0.8174 (mp) REVERT: A 710 ILE cc_start: 0.9017 (tt) cc_final: 0.8736 (tt) REVERT: A 859 ARG cc_start: 0.7678 (mmm160) cc_final: 0.6973 (mmp-170) REVERT: A 1126 LYS cc_start: 0.8516 (mmtt) cc_final: 0.7755 (mppt) REVERT: A 1150 ARG cc_start: 0.8394 (ttm110) cc_final: 0.8178 (ttp80) REVERT: A 1167 MET cc_start: 0.8300 (mtp) cc_final: 0.7673 (mtm) REVERT: A 1199 MET cc_start: 0.8113 (ptm) cc_final: 0.7731 (mmm) REVERT: A 1243 LEU cc_start: 0.8824 (mp) cc_final: 0.8607 (mt) outliers start: 19 outliers final: 6 residues processed: 97 average time/residue: 1.1352 time to fit residues: 118.3426 Evaluate side-chains 88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 GLU 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 994 SER Chi-restraints excluded: chain A residue 1090 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 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 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 = 0.3792 r_free = 0.3792 target = 0.141724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110874 restraints weight = 10803.686| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.49 r_work: 0.3248 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8493 Z= 0.162 Angle : 0.557 6.815 11572 Z= 0.277 Chirality : 0.042 0.138 1250 Planarity : 0.004 0.039 1506 Dihedral : 4.648 28.121 1214 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.39 % Allowed : 14.60 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.26), residues: 1022 helix: 1.35 (0.66), residues: 72 sheet: -0.22 (0.25), residues: 457 loop : -0.30 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE A 735 TYR 0.010 0.001 TYR A1054 ARG 0.004 0.000 ARG A 406 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 3) link_NAG-ASN : angle 2.39440 ( 9) link_BETA1-4 : bond 0.00879 ( 1) link_BETA1-4 : angle 1.20341 ( 3) hydrogen bonds : bond 0.03027 ( 268) hydrogen bonds : angle 5.43812 ( 714) SS BOND : bond 0.00248 ( 7) SS BOND : angle 0.68724 ( 14) covalent geometry : bond 0.00374 ( 8482) covalent geometry : angle 0.55246 (11546) *********************** 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 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8859 (tttp) cc_final: 0.8486 (tptp) REVERT: A 265 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7571 (mtmt) REVERT: A 266 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 384 ASP cc_start: 0.8323 (t70) cc_final: 0.8069 (t0) REVERT: A 406 ARG cc_start: 0.7906 (ttp-110) cc_final: 0.7691 (ttp-110) REVERT: A 462 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7644 (ttt-90) REVERT: A 550 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8470 (tpp-160) REVERT: A 553 MET cc_start: 0.8774 (mtm) cc_final: 0.7990 (mmm) REVERT: A 565 MET cc_start: 0.9070 (tpp) cc_final: 0.8377 (tpp) REVERT: A 600 GLU cc_start: 0.8339 (pp20) cc_final: 0.7905 (tm-30) REVERT: A 665 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7990 (mtmt) REVERT: A 710 ILE cc_start: 0.9100 (tt) cc_final: 0.8823 (tt) REVERT: A 1126 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7795 (mppt) REVERT: A 1150 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8196 (ttp80) REVERT: A 1167 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7770 (mtm) REVERT: A 1199 MET cc_start: 0.8129 (ptm) cc_final: 0.7771 (mmm) REVERT: A 1243 LEU cc_start: 0.8889 (mp) cc_final: 0.8680 (mt) outliers start: 21 outliers final: 8 residues processed: 104 average time/residue: 1.1837 time to fit residues: 131.6821 Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 HIS A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111087 restraints weight = 10743.964| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.53 r_work: 0.3252 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3223 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= 0.121 Angle : 0.538 6.019 11572 Z= 0.266 Chirality : 0.042 0.138 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.541 27.312 1214 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 15.62 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1022 helix: 1.54 (0.65), residues: 72 sheet: -0.18 (0.25), residues: 445 loop : -0.23 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 989 HIS 0.003 0.001 HIS A 459 PHE 0.012 0.001 PHE A 735 TYR 0.009 0.001 TYR A1054 ARG 0.006 0.000 ARG A 879 Details of bonding type rmsd link_NAG-ASN : bond 0.00208 ( 3) link_NAG-ASN : angle 3.66060 ( 9) link_BETA1-4 : bond 0.00794 ( 1) link_BETA1-4 : angle 1.56892 ( 3) hydrogen bonds : bond 0.02836 ( 268) hydrogen bonds : angle 5.32935 ( 714) SS BOND : bond 0.00222 ( 7) SS BOND : angle 0.64683 ( 14) covalent geometry : bond 0.00282 ( 8482) covalent geometry : angle 0.52799 (11546) *********************** 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 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8510 (t0) cc_final: 0.8226 (t0) REVERT: A 234 GLU cc_start: 0.8140 (pt0) cc_final: 0.7719 (pt0) REVERT: A 241 LYS cc_start: 0.8848 (tttp) cc_final: 0.8437 (tptp) REVERT: A 265 LYS cc_start: 0.7987 (mtpt) cc_final: 0.7471 (mtmt) REVERT: A 266 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 384 ASP cc_start: 0.8336 (t70) cc_final: 0.8042 (t70) REVERT: A 462 ARG cc_start: 0.8037 (ttt90) cc_final: 0.7558 (ttt-90) REVERT: A 600 GLU cc_start: 0.8337 (pp20) cc_final: 0.7948 (tm-30) REVERT: A 603 GLN cc_start: 0.8443 (mm110) cc_final: 0.8163 (mm110) REVERT: A 1126 LYS cc_start: 0.8554 (mmtt) cc_final: 0.7775 (mppt) REVERT: A 1150 ARG cc_start: 0.8373 (ttm110) cc_final: 0.8170 (ttp80) REVERT: A 1167 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7669 (mtm) REVERT: A 1199 MET cc_start: 0.8081 (ptm) cc_final: 0.7666 (mmm) REVERT: A 1243 LEU cc_start: 0.8884 (mp) cc_final: 0.8675 (mt) REVERT: A 1273 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8729 (p) outliers start: 19 outliers final: 7 residues processed: 105 average time/residue: 1.2259 time to fit residues: 137.6914 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 : 0.867 ------------------------------------------------------------------------------- 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 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 878 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS A1174 GLN A1229 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105457 restraints weight = 10821.075| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.69 r_work: 0.3197 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8493 Z= 0.188 Angle : 0.566 6.212 11572 Z= 0.281 Chirality : 0.043 0.148 1250 Planarity : 0.004 0.039 1506 Dihedral : 4.627 25.335 1214 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.74 % Allowed : 16.08 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.26), residues: 1022 helix: 1.39 (0.65), residues: 73 sheet: -0.19 (0.25), residues: 443 loop : -0.19 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 989 HIS 0.004 0.001 HIS A1063 PHE 0.014 0.002 PHE A 716 TYR 0.015 0.001 TYR A 567 ARG 0.006 0.000 ARG A 879 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 3) link_NAG-ASN : angle 2.59596 ( 9) link_BETA1-4 : bond 0.00897 ( 1) link_BETA1-4 : angle 1.10505 ( 3) hydrogen bonds : bond 0.03006 ( 268) hydrogen bonds : angle 5.38303 ( 714) SS BOND : bond 0.00260 ( 7) SS BOND : angle 0.81394 ( 14) covalent geometry : bond 0.00437 ( 8482) covalent geometry : angle 0.56146 (11546) *********************** 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 103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8530 (t0) cc_final: 0.8278 (t0) REVERT: A 234 GLU cc_start: 0.8176 (pt0) cc_final: 0.7763 (pt0) REVERT: A 241 LYS cc_start: 0.8860 (tttp) cc_final: 0.8519 (tptp) REVERT: A 265 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7587 (mtmt) REVERT: A 266 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 384 ASP cc_start: 0.8364 (t70) cc_final: 0.8073 (t70) REVERT: A 462 ARG cc_start: 0.8038 (ttt90) cc_final: 0.7569 (ttt-90) REVERT: A 553 MET cc_start: 0.8799 (mtm) cc_final: 0.8482 (mmm) REVERT: A 565 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8950 (tpp) REVERT: A 600 GLU cc_start: 0.8335 (pp20) cc_final: 0.7938 (pp20) REVERT: A 603 GLN cc_start: 0.8455 (mm110) cc_final: 0.8069 (mm110) REVERT: A 710 ILE cc_start: 0.9142 (tt) cc_final: 0.8851 (tt) REVERT: A 1126 LYS cc_start: 0.8578 (mmtt) cc_final: 0.7805 (mppt) REVERT: A 1150 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8219 (ttp80) REVERT: A 1167 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7790 (mtm) REVERT: A 1199 MET cc_start: 0.8137 (ptm) cc_final: 0.7757 (mmm) outliers start: 24 outliers final: 7 residues processed: 98 average time/residue: 1.1876 time to fit residues: 124.8408 Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1167 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 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 = 0.3763 r_free = 0.3763 target = 0.139807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.106046 restraints weight = 10940.180| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.67 r_work: 0.3208 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8493 Z= 0.177 Angle : 0.562 8.171 11572 Z= 0.277 Chirality : 0.043 0.156 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.546 23.197 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 16.53 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1022 helix: 1.47 (0.65), residues: 73 sheet: -0.18 (0.25), residues: 446 loop : -0.14 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.002 PHE A 716 TYR 0.015 0.001 TYR A 567 ARG 0.009 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 3) link_NAG-ASN : angle 2.30212 ( 9) link_BETA1-4 : bond 0.00827 ( 1) link_BETA1-4 : angle 0.79440 ( 3) hydrogen bonds : bond 0.02945 ( 268) hydrogen bonds : angle 5.33750 ( 714) SS BOND : bond 0.00265 ( 7) SS BOND : angle 0.82669 ( 14) covalent geometry : bond 0.00415 ( 8482) covalent geometry : angle 0.55805 (11546) *********************** 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 97 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8134 (pt0) cc_final: 0.7745 (pt0) REVERT: A 265 LYS cc_start: 0.7999 (mtpt) cc_final: 0.7489 (mtmt) REVERT: A 266 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 384 ASP cc_start: 0.8398 (t70) cc_final: 0.8104 (t70) REVERT: A 462 ARG cc_start: 0.7967 (ttt90) cc_final: 0.7462 (ttt-90) REVERT: A 527 GLN cc_start: 0.8210 (pt0) cc_final: 0.7925 (pm20) REVERT: A 549 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7572 (mmp80) REVERT: A 553 MET cc_start: 0.8811 (mtm) cc_final: 0.8329 (mmm) REVERT: A 565 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8866 (tpp) REVERT: A 600 GLU cc_start: 0.8382 (pp20) cc_final: 0.7967 (pp20) REVERT: A 603 GLN cc_start: 0.8417 (mm110) cc_final: 0.7988 (mm110) REVERT: A 668 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8158 (mm-30) REVERT: A 710 ILE cc_start: 0.9156 (tt) cc_final: 0.8826 (tt) REVERT: A 1126 LYS cc_start: 0.8594 (mmtt) cc_final: 0.7809 (mppt) REVERT: A 1167 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: A 1199 MET cc_start: 0.8075 (ptm) cc_final: 0.7692 (mmm) outliers start: 19 outliers final: 9 residues processed: 91 average time/residue: 1.2967 time to fit residues: 125.8418 Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1090 THR Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 3.9990 chunk 46 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS A1174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.105569 restraints weight = 10991.189| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.68 r_work: 0.3196 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 8493 Z= 0.195 Angle : 0.570 6.954 11572 Z= 0.281 Chirality : 0.043 0.154 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.576 21.893 1214 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.39 % Allowed : 16.76 % 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 (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: -0.19 (0.27), residues: 1022 helix: 1.43 (0.65), residues: 73 sheet: -0.20 (0.25), residues: 446 loop : -0.15 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 989 HIS 0.004 0.001 HIS A1063 PHE 0.014 0.002 PHE A 716 TYR 0.015 0.001 TYR A 567 ARG 0.007 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 3) link_NAG-ASN : angle 2.22665 ( 9) link_BETA1-4 : bond 0.00905 ( 1) link_BETA1-4 : angle 1.15161 ( 3) hydrogen bonds : bond 0.02967 ( 268) hydrogen bonds : angle 5.37586 ( 714) SS BOND : bond 0.00281 ( 7) SS BOND : angle 0.86607 ( 14) covalent geometry : bond 0.00457 ( 8482) covalent geometry : angle 0.56616 (11546) *********************** 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 98 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8137 (pt0) cc_final: 0.7815 (pt0) REVERT: A 265 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7590 (mtmt) REVERT: A 266 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7830 (mp0) REVERT: A 335 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7492 (ttm) REVERT: A 384 ASP cc_start: 0.8423 (t70) cc_final: 0.8178 (t70) REVERT: A 462 ARG cc_start: 0.8019 (ttt90) cc_final: 0.7548 (ttt-90) REVERT: A 527 GLN cc_start: 0.8224 (pt0) cc_final: 0.7995 (pm20) REVERT: A 549 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7583 (mmp80) REVERT: A 553 MET cc_start: 0.8793 (mtm) cc_final: 0.8368 (mmm) REVERT: A 565 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8878 (tpp) REVERT: A 600 GLU cc_start: 0.8389 (pp20) cc_final: 0.7992 (pp20) REVERT: A 603 GLN cc_start: 0.8438 (mm110) cc_final: 0.8189 (mm110) REVERT: A 710 ILE cc_start: 0.9171 (tt) cc_final: 0.8863 (tt) REVERT: A 1126 LYS cc_start: 0.8627 (mmtt) cc_final: 0.7853 (mppt) REVERT: A 1167 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7810 (mtm) REVERT: A 1199 MET cc_start: 0.8150 (ptm) cc_final: 0.7774 (mmm) outliers start: 21 outliers final: 11 residues processed: 90 average time/residue: 1.2732 time to fit residues: 122.7346 Evaluate side-chains 92 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1090 THR 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 65 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 0.0570 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106569 restraints weight = 10809.736| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.65 r_work: 0.3216 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8493 Z= 0.150 Angle : 0.551 7.267 11572 Z= 0.272 Chirality : 0.043 0.156 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.486 21.481 1214 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.82 % Allowed : 17.33 % 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 (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: -0.15 (0.27), residues: 1022 helix: 1.52 (0.64), residues: 73 sheet: -0.15 (0.26), residues: 442 loop : -0.15 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE A 886 TYR 0.016 0.001 TYR A 567 ARG 0.007 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 3) link_NAG-ASN : angle 2.20740 ( 9) link_BETA1-4 : bond 0.00771 ( 1) link_BETA1-4 : angle 1.25064 ( 3) hydrogen bonds : bond 0.02837 ( 268) hydrogen bonds : angle 5.31490 ( 714) SS BOND : bond 0.00249 ( 7) SS BOND : angle 0.81152 ( 14) covalent geometry : bond 0.00352 ( 8482) covalent geometry : angle 0.54671 (11546) ********************** 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 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8097 (pt0) cc_final: 0.7773 (pt0) REVERT: A 265 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7524 (mtmt) REVERT: A 266 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: A 384 ASP cc_start: 0.8398 (t70) cc_final: 0.8134 (t70) REVERT: A 462 ARG cc_start: 0.7936 (ttt90) cc_final: 0.7434 (ttt-90) REVERT: A 527 GLN cc_start: 0.8188 (pt0) cc_final: 0.7914 (pm20) REVERT: A 549 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7550 (mmp80) REVERT: A 553 MET cc_start: 0.8798 (mtm) cc_final: 0.8357 (mmm) REVERT: A 565 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8871 (tpp) REVERT: A 600 GLU cc_start: 0.8378 (pp20) cc_final: 0.7976 (pp20) REVERT: A 603 GLN cc_start: 0.8413 (mm110) cc_final: 0.8157 (mm110) REVERT: A 710 ILE cc_start: 0.9154 (tt) cc_final: 0.8840 (tt) REVERT: A 1126 LYS cc_start: 0.8644 (mmtt) cc_final: 0.7854 (mppt) REVERT: A 1167 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7724 (mtm) REVERT: A 1199 MET cc_start: 0.8121 (ptm) cc_final: 0.7731 (mmm) outliers start: 16 outliers final: 8 residues processed: 90 average time/residue: 1.4853 time to fit residues: 143.4513 Evaluate side-chains 88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 994 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 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 = 0.3761 r_free = 0.3761 target = 0.139606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106074 restraints weight = 10951.431| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.66 r_work: 0.3206 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8493 Z= 0.173 Angle : 0.565 7.145 11572 Z= 0.278 Chirality : 0.043 0.157 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.476 22.073 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.82 % Allowed : 17.45 % 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 (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 (0.27), residues: 1022 helix: 1.50 (0.64), residues: 73 sheet: -0.19 (0.25), residues: 454 loop : -0.08 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.002 PHE A 716 TYR 0.016 0.001 TYR A 567 ARG 0.008 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 3) link_NAG-ASN : angle 2.09039 ( 9) link_BETA1-4 : bond 0.00795 ( 1) link_BETA1-4 : angle 1.06106 ( 3) hydrogen bonds : bond 0.02899 ( 268) hydrogen bonds : angle 5.32558 ( 714) SS BOND : bond 0.00260 ( 7) SS BOND : angle 0.84296 ( 14) covalent geometry : bond 0.00405 ( 8482) covalent geometry : angle 0.56176 (11546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6982.18 seconds wall clock time: 120 minutes 11.04 seconds (7211.04 seconds total)