Starting phenix.real_space_refine on Wed Mar 12 23:24:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfp_44502/03_2025/9bfp_44502.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfp_44502/03_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_44502/03_2025/9bfp_44502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfp_44502/03_2025/9bfp_44502.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfp_44502/03_2025/9bfp_44502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfp_44502/03_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-5624/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: 5.79, per 1000 atoms: 0.70 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: 2.14 Conformation dependent library (CDL) restraints added in 990.7 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: 1.29 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: 2.55 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: 2.090 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: 0.060 Set scattering table: 0.090 Process input model: 24.520 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:12.570 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 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 : 0.950 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: 1.3078 time to fit residues: 217.9673 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 : 0.915 ------------------------------------------------------------------------------- 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 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 : 0.939 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: 1.2753 time to fit residues: 144.2174 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 : 0.874 ------------------------------------------------------------------------------- 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 8482 Z= 0.346 Angle : 0.640 7.122 11546 Z= 0.318 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 *********************** 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 : 0.941 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: 1.2071 time to fit residues: 135.6289 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 : 1.037 ------------------------------------------------------------------------------- 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 8482 Z= 0.245 Angle : 0.567 6.623 11546 Z= 0.282 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 *********************** 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 : 0.884 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: 1.1138 time to fit residues: 116.1977 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 : 0.938 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.141633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109750 restraints weight = 10801.445| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.58 r_work: 0.3228 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8482 Z= 0.251 Angle : 0.555 6.797 11546 Z= 0.277 Chirality : 0.043 0.152 1250 Planarity : 0.004 0.039 1506 Dihedral : 4.657 28.278 1214 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.28 % Allowed : 14.71 % 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 0.022 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 406 *********************** 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 109 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 241 LYS cc_start: 0.8872 (tttp) cc_final: 0.8492 (tptp) REVERT: A 265 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7505 (mtmt) REVERT: A 266 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7741 (mp0) REVERT: A 384 ASP cc_start: 0.8340 (t70) cc_final: 0.8057 (t0) REVERT: A 406 ARG cc_start: 0.7885 (ttp-110) cc_final: 0.7644 (ttp-110) REVERT: A 462 ARG cc_start: 0.8070 (ttt90) cc_final: 0.7616 (ttt-90) REVERT: A 550 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8456 (tpp-160) REVERT: A 553 MET cc_start: 0.8766 (mtm) cc_final: 0.8087 (mmm) REVERT: A 565 MET cc_start: 0.9069 (tpp) cc_final: 0.8447 (tpp) REVERT: A 600 GLU cc_start: 0.8352 (pp20) cc_final: 0.7906 (tm-30) REVERT: A 665 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7985 (mtmt) REVERT: A 710 ILE cc_start: 0.9090 (tt) cc_final: 0.8792 (tt) REVERT: A 1126 LYS cc_start: 0.8551 (mmtt) cc_final: 0.7770 (mppt) REVERT: A 1150 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8190 (ttp80) REVERT: A 1167 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: A 1199 MET cc_start: 0.8109 (ptm) cc_final: 0.7714 (mmm) REVERT: A 1243 LEU cc_start: 0.8872 (mp) cc_final: 0.8655 (mt) outliers start: 20 outliers final: 7 residues processed: 104 average time/residue: 1.1909 time to fit residues: 132.5191 Evaluate side-chains 88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 76 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.142718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111200 restraints weight = 10733.487| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.54 r_work: 0.3282 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8482 Z= 0.175 Angle : 0.524 6.023 11546 Z= 0.262 Chirality : 0.042 0.138 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.517 27.236 1214 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.05 % Allowed : 15.51 % Favored : 82.44 % 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: 1.55 (0.65), residues: 72 sheet: -0.17 (0.25), residues: 445 loop : -0.22 (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 0.008 0.001 TYR A1054 ARG 0.006 0.000 ARG A 879 *********************** 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 108 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8468 (t0) cc_final: 0.8181 (t0) REVERT: A 234 GLU cc_start: 0.8152 (pt0) cc_final: 0.7726 (pt0) REVERT: A 241 LYS cc_start: 0.8851 (tttp) cc_final: 0.8486 (tptt) REVERT: A 265 LYS cc_start: 0.8029 (mtpt) cc_final: 0.7525 (mtmt) REVERT: A 266 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: A 384 ASP cc_start: 0.8337 (t70) cc_final: 0.8076 (t70) REVERT: A 462 ARG cc_start: 0.8056 (ttt90) cc_final: 0.7595 (ttt-90) REVERT: A 550 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8326 (tpp-160) REVERT: A 565 MET cc_start: 0.9064 (tpp) cc_final: 0.8758 (tpp) REVERT: A 600 GLU cc_start: 0.8316 (pp20) cc_final: 0.7921 (pp20) REVERT: A 603 GLN cc_start: 0.8438 (mm110) cc_final: 0.8148 (mm110) REVERT: A 1094 GLN cc_start: 0.8408 (mt0) cc_final: 0.8009 (mt0) REVERT: A 1126 LYS cc_start: 0.8552 (mmtt) cc_final: 0.7783 (mppt) REVERT: A 1150 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8187 (ttp80) REVERT: A 1167 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7716 (mtm) REVERT: A 1199 MET cc_start: 0.8089 (ptm) cc_final: 0.7697 (mmm) REVERT: A 1243 LEU cc_start: 0.8885 (mp) cc_final: 0.8681 (mt) REVERT: A 1273 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8771 (p) outliers start: 18 outliers final: 5 residues processed: 103 average time/residue: 1.1750 time to fit residues: 129.6466 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 : 0.882 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 10 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.139373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105591 restraints weight = 10796.371| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.65 r_work: 0.3196 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8482 Z= 0.307 Angle : 0.574 7.958 11546 Z= 0.286 Chirality : 0.043 0.149 1250 Planarity : 0.004 0.039 1506 Dihedral : 4.665 25.367 1214 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.74 % Allowed : 15.85 % 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: -0.23 (0.26), residues: 1022 helix: 1.38 (0.65), residues: 73 sheet: -0.19 (0.25), residues: 445 loop : -0.22 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 989 HIS 0.004 0.001 HIS A1063 PHE 0.015 0.002 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 102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8497 (t0) cc_final: 0.8200 (t0) REVERT: A 234 GLU cc_start: 0.8163 (pt0) cc_final: 0.7741 (pt0) REVERT: A 241 LYS cc_start: 0.8870 (tttp) cc_final: 0.8523 (tptp) REVERT: A 265 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7520 (mtmt) REVERT: A 266 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: A 384 ASP cc_start: 0.8367 (t70) cc_final: 0.8074 (t70) REVERT: A 462 ARG cc_start: 0.8016 (ttt90) cc_final: 0.7527 (ttt-90) REVERT: A 550 ARG cc_start: 0.8716 (ttm110) cc_final: 0.8298 (tpp-160) REVERT: A 553 MET cc_start: 0.8757 (mtm) cc_final: 0.7921 (mmm) REVERT: A 565 MET cc_start: 0.9045 (tpp) cc_final: 0.8318 (tpp) REVERT: A 600 GLU cc_start: 0.8340 (pp20) cc_final: 0.7944 (pp20) REVERT: A 603 GLN cc_start: 0.8428 (mm110) cc_final: 0.8023 (mm110) REVERT: A 710 ILE cc_start: 0.9145 (tt) cc_final: 0.8831 (tt) REVERT: A 1126 LYS cc_start: 0.8575 (mmtt) cc_final: 0.7798 (mppt) REVERT: A 1150 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8187 (ttp80) REVERT: A 1167 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7719 (mtm) REVERT: A 1199 MET cc_start: 0.8107 (ptm) cc_final: 0.7715 (mmm) REVERT: A 1243 LEU cc_start: 0.8926 (mp) cc_final: 0.8722 (mt) REVERT: A 1273 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8743 (p) outliers start: 24 outliers final: 9 residues processed: 96 average time/residue: 1.1621 time to fit residues: 119.5824 Evaluate side-chains 90 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 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 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: 0.5980 chunk 31 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 79 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.140440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106257 restraints weight = 10934.123| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.71 r_work: 0.3214 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3447 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= 0.223 Angle : 0.536 6.772 11546 Z= 0.268 Chirality : 0.042 0.155 1250 Planarity : 0.004 0.042 1506 Dihedral : 4.522 24.764 1214 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.82 % Allowed : 16.42 % Favored : 81.76 % 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 (0.26), residues: 1022 helix: 1.51 (0.65), residues: 73 sheet: -0.18 (0.25), residues: 447 loop : -0.13 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 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 0.006 0.000 ARG A 879 *********************** 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 96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 233 ASP cc_start: 0.8485 (t0) cc_final: 0.8263 (t0) REVERT: A 234 GLU cc_start: 0.8154 (pt0) cc_final: 0.7751 (pt0) REVERT: A 241 LYS cc_start: 0.8858 (tttp) cc_final: 0.8505 (tptp) REVERT: A 265 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7558 (mtmt) REVERT: A 266 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: A 384 ASP cc_start: 0.8351 (t70) cc_final: 0.8101 (t70) REVERT: A 462 ARG cc_start: 0.8030 (ttt90) cc_final: 0.7530 (ttt-90) REVERT: A 527 GLN cc_start: 0.8239 (pt0) cc_final: 0.7992 (pm20) REVERT: A 550 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8354 (tpp-160) REVERT: A 553 MET cc_start: 0.8761 (mtm) cc_final: 0.7945 (mmm) REVERT: A 565 MET cc_start: 0.9040 (tpp) cc_final: 0.8313 (tpp) REVERT: A 600 GLU cc_start: 0.8374 (pp20) cc_final: 0.7964 (pp20) REVERT: A 603 GLN cc_start: 0.8432 (mm110) cc_final: 0.8069 (mm110) REVERT: A 710 ILE cc_start: 0.9157 (tt) cc_final: 0.8858 (tt) REVERT: A 882 ARG cc_start: 0.8731 (mmp80) cc_final: 0.8525 (mmp80) REVERT: A 1126 LYS cc_start: 0.8583 (mmtt) cc_final: 0.7814 (mppt) REVERT: A 1167 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.7778 (mtm) REVERT: A 1199 MET cc_start: 0.8116 (ptm) cc_final: 0.7764 (mmm) REVERT: A 1243 LEU cc_start: 0.8936 (mp) cc_final: 0.8735 (mt) outliers start: 16 outliers final: 9 residues processed: 93 average time/residue: 1.2400 time to fit residues: 123.3940 Evaluate side-chains 88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 588 LEU Chi-restraints excluded: chain A residue 610 GLN Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 708 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 73 optimal weight: 0.0770 chunk 46 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.140730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.107014 restraints weight = 10951.002| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.69 r_work: 0.3224 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 0.027 8482 Z= 0.210 Angle : 0.527 6.978 11546 Z= 0.262 Chirality : 0.042 0.155 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.385 21.433 1214 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 16.88 % 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: -0.14 (0.27), residues: 1022 helix: 1.62 (0.64), residues: 73 sheet: -0.19 (0.25), residues: 441 loop : -0.12 (0.27), residues: 508 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 0.017 0.001 TYR A 567 ARG 0.007 0.000 ARG A 879 *********************** 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 95 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8153 (pt0) cc_final: 0.7749 (pt0) REVERT: A 265 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7553 (mtmt) REVERT: A 266 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 384 ASP cc_start: 0.8384 (t70) cc_final: 0.8124 (t70) REVERT: A 462 ARG cc_start: 0.7959 (ttt90) cc_final: 0.7463 (ttt-90) REVERT: A 527 GLN cc_start: 0.8203 (pt0) cc_final: 0.7947 (pm20) REVERT: A 550 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8404 (tpp-160) REVERT: A 553 MET cc_start: 0.8745 (mtm) cc_final: 0.7916 (mmm) REVERT: A 565 MET cc_start: 0.9027 (tpp) cc_final: 0.8290 (tpp) REVERT: A 600 GLU cc_start: 0.8374 (pp20) cc_final: 0.7974 (pp20) REVERT: A 603 GLN cc_start: 0.8400 (mm110) cc_final: 0.7964 (mm110) REVERT: A 710 ILE cc_start: 0.9162 (tt) cc_final: 0.8865 (tt) REVERT: A 1126 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7836 (mppt) REVERT: A 1167 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7758 (mtm) REVERT: A 1199 MET cc_start: 0.8111 (ptm) cc_final: 0.7755 (mmm) outliers start: 17 outliers final: 10 residues processed: 91 average time/residue: 1.3635 time to fit residues: 132.5398 Evaluate side-chains 90 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 22 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 25 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.140630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106951 restraints weight = 10796.807| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.66 r_work: 0.3225 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8482 Z= 0.225 Angle : 0.537 7.261 11546 Z= 0.266 Chirality : 0.042 0.157 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.376 21.105 1214 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.71 % Allowed : 17.22 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.27), residues: 1022 helix: 1.66 (0.64), residues: 73 sheet: -0.12 (0.25), residues: 442 loop : -0.11 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 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 0.007 0.000 ARG A 879 ********************** 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: 15 poor density : 79 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 GLU cc_start: 0.8055 (pt0) cc_final: 0.7725 (pt0) REVERT: A 265 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7534 (mtmt) REVERT: A 266 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: A 384 ASP cc_start: 0.8403 (t70) cc_final: 0.8141 (t70) REVERT: A 462 ARG cc_start: 0.7932 (ttt90) cc_final: 0.7455 (ttt-90) REVERT: A 527 GLN cc_start: 0.8196 (pt0) cc_final: 0.7931 (pm20) REVERT: A 550 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8393 (tpp-160) REVERT: A 553 MET cc_start: 0.8735 (mtm) cc_final: 0.7898 (mmm) REVERT: A 565 MET cc_start: 0.9008 (tpp) cc_final: 0.8265 (tpp) REVERT: A 600 GLU cc_start: 0.8365 (pp20) cc_final: 0.7966 (pp20) REVERT: A 603 GLN cc_start: 0.8401 (mm110) cc_final: 0.8145 (mm110) REVERT: A 710 ILE cc_start: 0.9154 (tt) cc_final: 0.8853 (tt) REVERT: A 1039 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8343 (mt-10) REVERT: A 1126 LYS cc_start: 0.8631 (mmtt) cc_final: 0.7842 (mppt) REVERT: A 1167 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7747 (mtm) REVERT: A 1199 MET cc_start: 0.8110 (ptm) cc_final: 0.7729 (mmm) outliers start: 15 outliers final: 10 residues processed: 91 average time/residue: 1.3554 time to fit residues: 132.1321 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 : 0.942 ------------------------------------------------------------------------------- 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 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 1039 GLU Chi-restraints excluded: chain A residue 1057 SER Chi-restraints excluded: chain A residue 1146 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1174 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3776 r_free = 0.3776 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107341 restraints weight = 10914.992| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.68 r_work: 0.3230 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3549 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= 0.197 Angle : 0.529 7.274 11546 Z= 0.262 Chirality : 0.042 0.157 1250 Planarity : 0.004 0.041 1506 Dihedral : 4.332 20.975 1214 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.60 % Allowed : 17.45 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.06 (0.27), residues: 1022 helix: 1.79 (0.63), residues: 73 sheet: -0.14 (0.26), residues: 444 loop : -0.08 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 989 HIS 0.004 0.001 HIS A 459 PHE 0.012 0.001 PHE A 735 TYR 0.016 0.001 TYR A 567 ARG 0.007 0.000 ARG A 879 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6867.61 seconds wall clock time: 118 minutes 29.48 seconds (7109.48 seconds total)