Starting phenix.real_space_refine on Wed Feb 12 22:08:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfp_44502/02_2025/9bfp_44502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfp_44502/02_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_44502/02_2025/9bfp_44502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfp_44502/02_2025/9bfp_44502.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfp_44502/02_2025/9bfp_44502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfp_44502/02_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-5592/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: 5.35, per 1000 atoms: 0.65 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: 1.98 Conformation dependent library (CDL) restraints added in 927.0 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: 1.28 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: 3.60 Time building geometry restraints manager: 2.29 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: 4.330 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.900 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:11.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.630 ------------------------------------------------------------------------------- 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 8482 Z= 0.440 Angle : 1.235 16.916 11546 Z= 0.666 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 *********************** 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 : 0.933 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: 1.3554 time to fit residues: 225.4140 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 : 0.903 ------------------------------------------------------------------------------- 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 = 0.106948 restraints weight = 10122.220| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.65 r_work: 0.3128 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 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 8482 Z= 0.209 Angle : 0.615 6.637 11546 Z= 0.312 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 *********************** 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 : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7791 (mtmt) REVERT: A 462 ARG cc_start: 0.7777 (ttt90) cc_final: 0.7090 (tmt-80) REVERT: A 603 GLN cc_start: 0.8334 (mm110) cc_final: 0.8010 (mm110) REVERT: A 719 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: A 882 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8129 (mmp80) REVERT: A 1120 GLN cc_start: 0.7273 (mp10) cc_final: 0.6881 (mp10) REVERT: A 1150 ARG cc_start: 0.8205 (ttm110) cc_final: 0.7992 (ttp80) REVERT: A 1167 MET cc_start: 0.8175 (mtp) cc_final: 0.7568 (mtm) REVERT: A 1199 MET cc_start: 0.8031 (ptm) cc_final: 0.7772 (mmm) outliers start: 17 outliers final: 2 residues processed: 106 average time/residue: 1.3395 time to fit residues: 150.9849 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 : 0.987 ------------------------------------------------------------------------------- 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: 0.6980 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: 0.0370 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: 1.0662 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.141810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110111 restraints weight = 10867.288| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.54 r_work: 0.3234 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8482 Z= 0.325 Angle : 0.628 7.500 11546 Z= 0.313 Chirality : 0.044 0.172 1250 Planarity : 0.005 0.041 1506 Dihedral : 5.129 28.576 1214 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.83 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: 0.49 (0.65), residues: 72 sheet: -0.35 (0.24), residues: 453 loop : -0.61 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 333 HIS 0.005 0.001 HIS A 986 PHE 0.018 0.002 PHE A 413 TYR 0.022 0.002 TYR A 740 ARG 0.007 0.001 ARG A 492 *********************** 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: 24 poor density : 89 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7563 (mtmt) REVERT: A 266 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: A 384 ASP cc_start: 0.8215 (t70) cc_final: 0.7979 (t0) REVERT: A 462 ARG cc_start: 0.8022 (ttt90) cc_final: 0.7184 (ttt-90) REVERT: A 485 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: A 553 MET cc_start: 0.8727 (mmm) cc_final: 0.8102 (mmt) REVERT: A 600 GLU cc_start: 0.8322 (pp20) cc_final: 0.8025 (pp20) REVERT: A 603 GLN cc_start: 0.8435 (mm110) cc_final: 0.8195 (mm110) REVERT: A 665 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7939 (mtmt) REVERT: A 710 ILE cc_start: 0.8996 (tt) cc_final: 0.8725 (tt) REVERT: A 859 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7005 (mmp-170) REVERT: A 1126 LYS cc_start: 0.8504 (mmtt) cc_final: 0.7747 (mppt) REVERT: A 1150 ARG cc_start: 0.8402 (ttm110) cc_final: 0.8187 (ttp80) REVERT: A 1167 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7623 (mtm) REVERT: A 1199 MET cc_start: 0.8139 (ptm) cc_final: 0.7752 (mmm) REVERT: A 1243 LEU cc_start: 0.8817 (mp) cc_final: 0.8570 (mt) outliers start: 24 outliers final: 5 residues processed: 103 average time/residue: 1.2699 time to fit residues: 139.6737 Evaluate side-chains 86 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 485 GLU 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: 7.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 A1174 GLN A1229 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108515 restraints weight = 10835.657| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.54 r_work: 0.3207 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8482 Z= 0.350 Angle : 0.611 6.928 11546 Z= 0.303 Chirality : 0.044 0.155 1250 Planarity : 0.004 0.039 1506 Dihedral : 5.057 30.201 1214 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 13.34 % Favored : 84.04 % 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: -0.60 (0.26), residues: 1022 helix: 0.72 (0.66), residues: 73 sheet: -0.39 (0.24), residues: 457 loop : -0.43 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 989 HIS 0.005 0.001 HIS A1063 PHE 0.014 0.002 PHE A 409 TYR 0.015 0.001 TYR A 740 ARG 0.005 0.000 ARG A 492 *********************** 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 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 265 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7605 (mtmt) REVERT: A 266 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7810 (mp0) REVERT: A 384 ASP cc_start: 0.8319 (t70) cc_final: 0.8084 (t0) REVERT: A 462 ARG cc_start: 0.8061 (ttt90) cc_final: 0.7516 (ttt-90) REVERT: A 553 MET cc_start: 0.8729 (mmm) cc_final: 0.8066 (mmt) REVERT: A 600 GLU cc_start: 0.8324 (pp20) cc_final: 0.7917 (tm-30) REVERT: A 603 GLN cc_start: 0.8478 (mm110) cc_final: 0.8153 (mm110) REVERT: A 665 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8103 (mtmt) REVERT: A 704 ILE cc_start: 0.8407 (mp) cc_final: 0.8206 (mp) REVERT: A 710 ILE cc_start: 0.9067 (tt) cc_final: 0.8777 (tt) REVERT: A 859 ARG cc_start: 0.7708 (mmm160) cc_final: 0.6988 (mmp-170) REVERT: A 1094 GLN cc_start: 0.8520 (mt0) cc_final: 0.8065 (mt0) REVERT: A 1126 LYS cc_start: 0.8567 (mmtt) cc_final: 0.7815 (mppt) REVERT: A 1150 ARG cc_start: 0.8418 (ttm110) cc_final: 0.8214 (ttp80) REVERT: A 1167 MET cc_start: 0.8398 (mtp) cc_final: 0.7763 (mtm) REVERT: A 1199 MET cc_start: 0.8169 (ptm) cc_final: 0.7770 (mmm) REVERT: A 1243 LEU cc_start: 0.8881 (mp) cc_final: 0.8658 (mt) outliers start: 23 outliers final: 7 residues processed: 104 average time/residue: 1.3643 time to fit residues: 150.6488 Evaluate side-chains 85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 1174 GLN 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: 1.9990 chunk 76 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3787 r_free = 0.3787 target = 0.141196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109536 restraints weight = 10794.846| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.55 r_work: 0.3228 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8482 Z= 0.253 Angle : 0.569 8.682 11546 Z= 0.281 Chirality : 0.043 0.146 1250 Planarity : 0.004 0.039 1506 Dihedral : 4.779 29.649 1214 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.51 % Allowed : 14.60 % Favored : 82.90 % 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: -0.45 (0.26), residues: 1022 helix: 1.09 (0.66), residues: 73 sheet: -0.33 (0.24), residues: 453 loop : -0.34 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.013 0.001 PHE A 716 TYR 0.010 0.001 TYR A1054 ARG 0.006 0.000 ARG A 549 *********************** 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 111 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8480 (t0) cc_final: 0.8261 (t0) REVERT: A 265 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7563 (mtmt) REVERT: A 384 ASP cc_start: 0.8342 (t70) cc_final: 0.8057 (t70) REVERT: A 406 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7649 (ttp-110) REVERT: A 462 ARG cc_start: 0.8053 (ttt90) cc_final: 0.7480 (ttt-90) REVERT: A 600 GLU cc_start: 0.8342 (pp20) cc_final: 0.7904 (tm-30) REVERT: A 704 ILE cc_start: 0.8397 (mp) cc_final: 0.8190 (mp) REVERT: A 710 ILE cc_start: 0.9107 (tt) cc_final: 0.8818 (tt) REVERT: A 1126 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7782 (mppt) REVERT: A 1150 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8185 (ttp80) REVERT: A 1167 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7718 (mtm) REVERT: A 1199 MET cc_start: 0.8117 (ptm) cc_final: 0.7719 (mmm) REVERT: A 1243 LEU cc_start: 0.8878 (mp) cc_final: 0.8662 (mt) outliers start: 22 outliers final: 9 residues processed: 105 average time/residue: 1.1894 time to fit residues: 134.0047 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 : 1.003 ------------------------------------------------------------------------------- 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 610 GLN Chi-restraints excluded: chain A residue 709 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 64 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.0970 chunk 83 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 25 optimal weight: 0.0470 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 568 GLN A 726 HIS A1174 GLN A1229 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.143220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111922 restraints weight = 10727.687| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.52 r_work: 0.3263 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8482 Z= 0.154 Angle : 0.522 6.814 11546 Z= 0.260 Chirality : 0.041 0.139 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.547 27.503 1214 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.71 % Allowed : 16.31 % Favored : 81.98 % 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: -0.25 (0.26), residues: 1022 helix: 1.47 (0.65), residues: 72 sheet: -0.20 (0.25), residues: 445 loop : -0.24 (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 0.017 0.001 TYR A 567 ARG 0.007 0.000 ARG A 549 *********************** 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 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.879 Fit side-chains REVERT: A 233 ASP cc_start: 0.8505 (t0) cc_final: 0.8278 (t0) REVERT: A 234 GLU cc_start: 0.8133 (pt0) cc_final: 0.7737 (pt0) REVERT: A 265 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7465 (mtmt) REVERT: A 384 ASP cc_start: 0.8319 (t70) cc_final: 0.8032 (t70) REVERT: A 462 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7591 (ttt-90) REVERT: A 485 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7540 (tp30) REVERT: A 553 MET cc_start: 0.8760 (mtm) cc_final: 0.8391 (mmm) REVERT: A 600 GLU cc_start: 0.8343 (pp20) cc_final: 0.7976 (pp20) REVERT: A 603 GLN cc_start: 0.8455 (mm110) cc_final: 0.8141 (mm110) REVERT: A 704 ILE cc_start: 0.8369 (mp) cc_final: 0.8144 (mp) REVERT: A 710 ILE cc_start: 0.9087 (tt) cc_final: 0.8801 (tt) REVERT: A 1094 GLN cc_start: 0.8388 (mt0) cc_final: 0.8036 (mt0) REVERT: A 1126 LYS cc_start: 0.8536 (mmtt) cc_final: 0.7751 (mppt) REVERT: A 1167 MET cc_start: 0.8303 (mtp) cc_final: 0.7660 (mtm) REVERT: A 1199 MET cc_start: 0.8083 (ptm) cc_final: 0.7666 (mmm) REVERT: A 1243 LEU cc_start: 0.8876 (mp) cc_final: 0.8670 (mt) REVERT: A 1273 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8736 (p) outliers start: 15 outliers final: 9 residues processed: 102 average time/residue: 1.2487 time to fit residues: 135.8616 Evaluate side-chains 87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 485 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 981 CYS Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1174 GLN 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: 0.7980 chunk 102 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 19 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.140464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106871 restraints weight = 10757.634| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.65 r_work: 0.3216 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8482 Z= 0.246 Angle : 0.545 7.814 11546 Z= 0.271 Chirality : 0.042 0.144 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.546 25.425 1214 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.39 % Allowed : 16.31 % 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: -0.23 (0.26), residues: 1022 helix: 1.48 (0.65), residues: 73 sheet: -0.21 (0.25), residues: 445 loop : -0.21 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 989 HIS 0.003 0.001 HIS A 459 PHE 0.013 0.001 PHE A 716 TYR 0.016 0.001 TYR A 567 ARG 0.006 0.000 ARG A 879 *********************** 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 99 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8474 (t0) cc_final: 0.8207 (t0) REVERT: A 234 GLU cc_start: 0.8097 (pt0) cc_final: 0.7691 (pt0) REVERT: A 265 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7421 (mtmt) REVERT: A 266 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 384 ASP cc_start: 0.8334 (t70) cc_final: 0.8009 (t70) REVERT: A 462 ARG cc_start: 0.8011 (ttt90) cc_final: 0.7552 (ttt-90) REVERT: A 485 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: A 600 GLU cc_start: 0.8345 (pp20) cc_final: 0.7949 (pp20) REVERT: A 603 GLN cc_start: 0.8426 (mm110) cc_final: 0.8082 (mm110) REVERT: A 710 ILE cc_start: 0.9117 (tt) cc_final: 0.8803 (tt) REVERT: A 1126 LYS cc_start: 0.8562 (mmtt) cc_final: 0.7748 (mppt) REVERT: A 1167 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7630 (mtm) REVERT: A 1199 MET cc_start: 0.8041 (ptm) cc_final: 0.7610 (mmm) REVERT: A 1243 LEU cc_start: 0.8878 (mp) cc_final: 0.8669 (mt) REVERT: A 1273 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (p) outliers start: 21 outliers final: 10 residues processed: 95 average time/residue: 1.2894 time to fit residues: 130.4822 Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 426 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 485 GLU 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 709 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 67 optimal weight: 0.0570 chunk 24 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.141654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.108083 restraints weight = 10892.317| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.67 r_work: 0.3242 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8482 Z= 0.181 Angle : 0.516 6.716 11546 Z= 0.258 Chirality : 0.042 0.155 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.383 23.382 1214 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.17 % Allowed : 16.42 % Favored : 81.41 % 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: -0.10 (0.27), residues: 1022 helix: 1.69 (0.63), residues: 77 sheet: -0.22 (0.25), residues: 438 loop : -0.04 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 989 HIS 0.003 0.001 HIS A 459 PHE 0.011 0.001 PHE A 735 TYR 0.016 0.001 TYR A 567 ARG 0.008 0.000 ARG A 549 *********************** 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 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.916 Fit side-chains REVERT: A 233 ASP cc_start: 0.8499 (t0) cc_final: 0.8272 (t0) REVERT: A 234 GLU cc_start: 0.8098 (pt0) cc_final: 0.7690 (pt0) REVERT: A 265 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7452 (mtmt) REVERT: A 266 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 384 ASP cc_start: 0.8324 (t70) cc_final: 0.8038 (t0) REVERT: A 462 ARG cc_start: 0.7998 (ttt90) cc_final: 0.7517 (ttt-90) REVERT: A 485 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: A 527 GLN cc_start: 0.8186 (pt0) cc_final: 0.7891 (pm20) REVERT: A 550 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.8459 (tpp-160) REVERT: A 600 GLU cc_start: 0.8364 (pp20) cc_final: 0.7955 (pp20) REVERT: A 603 GLN cc_start: 0.8399 (mm110) cc_final: 0.8031 (mm110) REVERT: A 610 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8042 (tm-30) REVERT: A 710 ILE cc_start: 0.9118 (tt) cc_final: 0.8818 (tt) REVERT: A 1094 GLN cc_start: 0.8481 (mt0) cc_final: 0.8023 (mt0) REVERT: A 1126 LYS cc_start: 0.8565 (mmtt) cc_final: 0.7759 (mppt) REVERT: A 1167 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: A 1199 MET cc_start: 0.8052 (ptm) cc_final: 0.7665 (mmm) REVERT: A 1273 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8726 (p) outliers start: 19 outliers final: 7 residues processed: 96 average time/residue: 1.2350 time to fit residues: 126.8062 Evaluate side-chains 89 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 426 THR Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 728 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 0.0050 chunk 46 optimal weight: 0.0000 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.0000 chunk 54 optimal weight: 0.0370 chunk 44 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 0.1480 ------------------------------------------------------------------------------- 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 568 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.111332 restraints weight = 10856.661| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.69 r_work: 0.3293 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8482 Z= 0.121 Angle : 0.506 8.373 11546 Z= 0.252 Chirality : 0.041 0.157 1250 Planarity : 0.004 0.042 1506 Dihedral : 4.095 19.161 1214 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.25 % Allowed : 17.67 % 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 (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: 0.09 (0.27), residues: 1022 helix: 2.26 (0.62), residues: 76 sheet: -0.07 (0.26), residues: 432 loop : -0.03 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 989 HIS 0.003 0.000 HIS A 459 PHE 0.013 0.001 PHE A 735 TYR 0.016 0.001 TYR A 567 ARG 0.009 0.000 ARG A 549 *********************** 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 97 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8010 (pt0) cc_final: 0.7613 (pt0) REVERT: A 265 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7352 (mtmt) REVERT: A 384 ASP cc_start: 0.8319 (t70) cc_final: 0.8009 (t0) REVERT: A 462 ARG cc_start: 0.7768 (ttt90) cc_final: 0.7243 (ttt-90) REVERT: A 527 GLN cc_start: 0.8171 (pt0) cc_final: 0.7837 (pm20) REVERT: A 550 ARG cc_start: 0.8649 (tpp-160) cc_final: 0.8437 (tpp-160) REVERT: A 600 GLU cc_start: 0.8380 (pp20) cc_final: 0.8017 (pp20) REVERT: A 603 GLN cc_start: 0.8374 (mm110) cc_final: 0.7993 (mm110) REVERT: A 610 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: A 710 ILE cc_start: 0.9096 (tt) cc_final: 0.8800 (tt) REVERT: A 860 SER cc_start: 0.7955 (m) cc_final: 0.7623 (p) REVERT: A 882 ARG cc_start: 0.8745 (mmp80) cc_final: 0.8448 (mmm160) REVERT: A 1039 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8399 (mp0) REVERT: A 1120 GLN cc_start: 0.7391 (mp10) cc_final: 0.6618 (mp10) REVERT: A 1167 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7950 (mpp) REVERT: A 1199 MET cc_start: 0.8039 (ptm) cc_final: 0.7616 (mmm) REVERT: A 1273 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8700 (p) outliers start: 11 outliers final: 3 residues processed: 94 average time/residue: 1.2171 time to fit residues: 122.3627 Evaluate side-chains 87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 994 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 0.0020 chunk 22 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3790 r_free = 0.3790 target = 0.142185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108680 restraints weight = 10767.255| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.67 r_work: 0.3252 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8482 Z= 0.199 Angle : 0.526 7.760 11546 Z= 0.261 Chirality : 0.042 0.159 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.181 19.250 1214 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.14 % Allowed : 18.02 % 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: 0.16 (0.27), residues: 1022 helix: 2.25 (0.62), residues: 76 sheet: -0.02 (0.26), residues: 441 loop : 0.03 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.012 0.001 PHE A 716 TYR 0.016 0.001 TYR A 567 ARG 0.008 0.000 ARG A 549 ********************** 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 87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8083 (pt0) cc_final: 0.7734 (pt0) REVERT: A 265 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7564 (mtmt) REVERT: A 384 ASP cc_start: 0.8352 (t70) cc_final: 0.8092 (t0) REVERT: A 462 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7335 (ttt-90) REVERT: A 527 GLN cc_start: 0.8168 (pt0) cc_final: 0.7920 (pm20) REVERT: A 550 ARG cc_start: 0.8686 (tpp-160) cc_final: 0.8470 (tpp-160) REVERT: A 600 GLU cc_start: 0.8384 (pp20) cc_final: 0.7992 (pp20) REVERT: A 603 GLN cc_start: 0.8373 (mm110) cc_final: 0.7992 (mm110) REVERT: A 610 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: A 710 ILE cc_start: 0.9136 (tt) cc_final: 0.8860 (tt) REVERT: A 860 SER cc_start: 0.8016 (m) cc_final: 0.7686 (p) REVERT: A 882 ARG cc_start: 0.8750 (mmp80) cc_final: 0.8341 (mmm160) REVERT: A 1167 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8126 (mpp) REVERT: A 1199 MET cc_start: 0.8105 (ptm) cc_final: 0.7723 (mmm) REVERT: A 1273 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8766 (p) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 1.2021 time to fit residues: 109.7496 Evaluate side-chains 84 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 THR 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 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1273 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3800 r_free = 0.3800 target = 0.142958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109378 restraints weight = 10849.051| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.70 r_work: 0.3273 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8482 Z= 0.162 Angle : 0.518 7.646 11546 Z= 0.258 Chirality : 0.042 0.160 1250 Planarity : 0.004 0.040 1506 Dihedral : 4.113 19.055 1214 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.48 % Allowed : 17.67 % 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: 0.21 (0.27), residues: 1022 helix: 2.39 (0.62), residues: 76 sheet: -0.00 (0.26), residues: 441 loop : 0.06 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 989 HIS 0.003 0.001 HIS A 459 PHE 0.013 0.001 PHE A 735 TYR 0.018 0.001 TYR A 567 ARG 0.008 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6510.26 seconds wall clock time: 115 minutes 15.53 seconds (6915.53 seconds total)