Starting phenix.real_space_refine on Sat Aug 23 03:45:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9fx2_50841/08_2025/9fx2_50841.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 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 28 5.16 5 C 5974 2.51 5 N 1515 2.21 5 O 1794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9311 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9241 Classifications: {'peptide': 1170} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1116} Chain breaks: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 2.29, per 1000 atoms: 0.25 Number of scatterers: 9311 At special positions: 0 Unit cell: (91.874, 126.812, 116.46, 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 28 16.00 O 1794 8.00 N 1515 7.00 C 5974 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 636 " 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 NAG-ASN " NAG A1301 " - " ASN A 41 " " NAG A1302 " - " ASN A 118 " " NAG A1303 " - " ASN A1244 " " NAG A1304 " - " ASN A 365 " " NAG A1305 " - " ASN A 419 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 377.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2212 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 18 sheets defined 21.5% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 301 through 306 removed outlier: 4.239A pdb=" N SER A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.628A pdb=" N ARG A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 606 through 618 Processing helix chain 'A' and resid 627 through 635 removed outlier: 3.908A pdb=" N PHE A 633 " --> pdb=" O SER A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 914 removed outlier: 3.700A pdb=" N LEU A 914 " --> pdb=" O GLY A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 943 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 946 through 967 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 985 through 1000 Processing helix chain 'A' and resid 1006 through 1020 removed outlier: 3.879A pdb=" N HIS A1020 " --> pdb=" O TRP A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1044 through 1057 Processing helix chain 'A' and resid 1058 through 1062 removed outlier: 3.574A pdb=" N LYS A1061 " --> pdb=" O GLY A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1082 Processing helix chain 'A' and resid 1085 through 1099 Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 4.475A pdb=" N GLU A1106 " --> pdb=" O PRO A1102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A1114 " --> pdb=" O MET A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1155 Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1161 through 1171 Processing helix chain 'A' and resid 1181 through 1198 removed outlier: 3.833A pdb=" N THR A1185 " --> pdb=" O THR A1181 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A1198 " --> pdb=" O PHE A1194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 7.432A pdb=" N THR A 43 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 removed outlier: 4.580A pdb=" N TYR A 102 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 74 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 135 Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 140 removed outlier: 5.290A pdb=" N LEU A 164 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 229 through 234 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 240 removed outlier: 6.281A pdb=" N CYS A 239 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 354 Processing sheet with id=AA8, first strand: chain 'A' and resid 413 through 420 Processing sheet with id=AA9, first strand: chain 'A' and resid 468 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 512 removed outlier: 6.451A pdb=" N VAL A 500 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL A 509 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR A 498 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS A 511 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 496 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 559 through 563 Processing sheet with id=AB3, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB4, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 Processing sheet with id=AB6, first strand: chain 'A' and resid 757 through 759 removed outlier: 6.133A pdb=" N VAL A 758 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 856 through 868 removed outlier: 4.404A pdb=" N VAL A 895 " --> pdb=" O LEU A1235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 875 through 882 removed outlier: 6.311A pdb=" N GLY A1211 " --> pdb=" O SER A1216 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N SER A1216 " --> pdb=" O GLY A1211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1116 through 1117 removed outlier: 3.566A pdb=" N PHE A1123 " --> pdb=" O GLU A1116 " (cutoff:3.500A) 445 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2940 1.34 - 1.46: 2180 1.46 - 1.58: 4339 1.58 - 1.70: 0 1.70 - 1.82: 49 Bond restraints: 9508 Sorted by residual: bond pdb=" C THR A 421 " pdb=" N VAL A 422 " ideal model delta sigma weight residual 1.329 1.480 -0.151 1.13e-02 7.83e+03 1.78e+02 bond pdb=" N ASN A 388 " pdb=" CA ASN A 388 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.30e+00 bond pdb=" N ASN A 365 " pdb=" CA ASN A 365 " ideal model delta sigma weight residual 1.456 1.484 -0.027 1.24e-02 6.50e+03 4.88e+00 bond pdb=" N PHE A 366 " pdb=" CA PHE A 366 " ideal model delta sigma weight residual 1.455 1.484 -0.028 1.30e-02 5.92e+03 4.79e+00 bond pdb=" N LEU A 364 " pdb=" CA LEU A 364 " ideal model delta sigma weight residual 1.461 1.484 -0.023 1.19e-02 7.06e+03 3.85e+00 ... (remaining 9503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 12696 2.46 - 4.92: 172 4.92 - 7.37: 37 7.37 - 9.83: 9 9.83 - 12.29: 3 Bond angle restraints: 12917 Sorted by residual: angle pdb=" CA LYS A 417 " pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" O VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLN A 416 " ideal model delta sigma weight residual 123.20 127.73 -4.53 1.06e+00 8.90e-01 1.83e+01 angle pdb=" CB LYS A 417 " pdb=" CG LYS A 417 " pdb=" CD LYS A 417 " ideal model delta sigma weight residual 111.30 121.08 -9.78 2.30e+00 1.89e-01 1.81e+01 angle pdb=" CA MET A 957 " pdb=" CB MET A 957 " pdb=" CG MET A 957 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA VAL A 415 " pdb=" C VAL A 415 " pdb=" N GLN A 416 " ideal model delta sigma weight residual 116.38 111.70 4.68 1.13e+00 7.83e-01 1.72e+01 ... (remaining 12912 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5095 17.89 - 35.78: 516 35.78 - 53.68: 116 53.68 - 71.57: 36 71.57 - 89.46: 7 Dihedral angle restraints: 5770 sinusoidal: 2351 harmonic: 3419 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 636 " pdb=" CB CYS A 636 " ideal model delta sinusoidal sigma weight residual -86.00 -151.66 65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CA MET A 625 " pdb=" C MET A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual 180.00 155.14 24.86 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA LEU A 48 " pdb=" C LEU A 48 " pdb=" N LEU A 49 " pdb=" CA LEU A 49 " ideal model delta harmonic sigma weight residual 180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 1515 0.180 - 0.361: 1 0.361 - 0.541: 0 0.541 - 0.721: 0 0.721 - 0.902: 1 Chirality restraints: 1517 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 419 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CB ILE A1052 " pdb=" CA ILE A1052 " pdb=" CG1 ILE A1052 " pdb=" CG2 ILE A1052 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.81e-01 chirality pdb=" CA ILE A 750 " pdb=" N ILE A 750 " pdb=" C ILE A 750 " pdb=" CB ILE A 750 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 1514 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " 0.189 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" C7 NAG A1304 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " 0.133 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " -0.266 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 415 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C VAL A 415 " -0.032 2.00e-02 2.50e+03 pdb=" O VAL A 415 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 416 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 419 " -0.002 2.00e-02 2.50e+03 1.53e-02 2.94e+00 pdb=" CG ASN A 419 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 419 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 419 " 0.021 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " -0.016 2.00e-02 2.50e+03 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1930 2.79 - 3.32: 8342 3.32 - 3.84: 15295 3.84 - 4.37: 17556 4.37 - 4.90: 30500 Nonbonded interactions: 73623 Sorted by model distance: nonbonded pdb=" NZ LYS A 161 " pdb=" OE2 GLU A 729 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 72 " pdb=" OE2 GLU A 75 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR A 860 " pdb=" OE1 GLN A 862 " model vdw 2.296 3.040 nonbonded pdb=" OD1 ASP A 136 " pdb=" OH TYR A 140 " model vdw 2.298 3.040 nonbonded pdb=" ND2 ASN A 388 " pdb=" ND2 ASN A 419 " model vdw 2.300 3.200 ... (remaining 73618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.230 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.005 0.151 9514 Z= 0.238 Angle : 0.844 22.118 12934 Z= 0.416 Chirality : 0.054 0.902 1517 Planarity : 0.005 0.159 1628 Dihedral : 15.544 89.461 3555 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.90 % Favored : 98.02 % Rotamer: Outliers : 0.19 % Allowed : 17.73 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.24), residues: 1160 helix: 0.62 (0.35), residues: 209 sheet: 0.52 (0.24), residues: 476 loop : -0.53 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 149 TYR 0.010 0.001 TYR A1002 PHE 0.014 0.001 PHE A 366 TRP 0.008 0.001 TRP A1167 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 9508) covalent geometry : angle 0.80113 (12917) SS BOND : bond 0.00122 ( 1) SS BOND : angle 1.56947 ( 2) hydrogen bonds : bond 0.10309 ( 438) hydrogen bonds : angle 5.14194 ( 1236) link_NAG-ASN : bond 0.01670 ( 5) link_NAG-ASN : angle 7.79127 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8381 (mm) outliers start: 2 outliers final: 0 residues processed: 35 average time/residue: 0.0955 time to fit residues: 5.1754 Evaluate side-chains 32 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 6.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A1157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.040615 restraints weight = 41088.079| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 4.12 r_work: 0.2746 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9514 Z= 0.225 Angle : 0.585 14.614 12934 Z= 0.290 Chirality : 0.046 0.622 1517 Planarity : 0.003 0.040 1628 Dihedral : 5.583 53.045 1350 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.33 % Favored : 97.59 % Rotamer: Outliers : 2.00 % Allowed : 17.06 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1160 helix: 1.20 (0.35), residues: 218 sheet: 0.69 (0.24), residues: 483 loop : -0.48 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1060 TYR 0.011 0.001 TYR A1002 PHE 0.033 0.002 PHE A 996 TRP 0.013 0.001 TRP A1124 HIS 0.003 0.001 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 9508) covalent geometry : angle 0.55761 (12917) SS BOND : bond 0.00305 ( 1) SS BOND : angle 2.31071 ( 2) hydrogen bonds : bond 0.03144 ( 438) hydrogen bonds : angle 4.73357 ( 1236) link_NAG-ASN : bond 0.00835 ( 5) link_NAG-ASN : angle 5.12947 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 30 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8974 (t0) cc_final: 0.8767 (t0) REVERT: A 125 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.7926 (mp0) REVERT: A 1110 MET cc_start: 0.8936 (ppp) cc_final: 0.8574 (ppp) outliers start: 21 outliers final: 14 residues processed: 50 average time/residue: 0.0786 time to fit residues: 6.1642 Evaluate side-chains 45 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 30 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1143 GLU Chi-restraints excluded: chain A residue 1165 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.066041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.042129 restraints weight = 39857.522| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.04 r_work: 0.2803 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9514 Z= 0.100 Angle : 0.498 12.920 12934 Z= 0.247 Chirality : 0.045 0.541 1517 Planarity : 0.003 0.041 1628 Dihedral : 5.112 49.480 1348 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.19 % Allowed : 17.54 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.25), residues: 1160 helix: 1.48 (0.35), residues: 218 sheet: 0.77 (0.24), residues: 489 loop : -0.31 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1060 TYR 0.008 0.001 TYR A 617 PHE 0.011 0.001 PHE A 219 TRP 0.008 0.001 TRP A1124 HIS 0.001 0.000 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9508) covalent geometry : angle 0.47602 (12917) SS BOND : bond 0.00004 ( 1) SS BOND : angle 1.24226 ( 2) hydrogen bonds : bond 0.02692 ( 438) hydrogen bonds : angle 4.45304 ( 1236) link_NAG-ASN : bond 0.00684 ( 5) link_NAG-ASN : angle 4.34587 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 29 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8895 (t0) cc_final: 0.8665 (t0) REVERT: A 125 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: A 848 MET cc_start: 0.8924 (mmm) cc_final: 0.8666 (mmm) REVERT: A 1110 MET cc_start: 0.8929 (ppp) cc_final: 0.8552 (ppp) REVERT: A 1171 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8860 (mm-40) outliers start: 23 outliers final: 11 residues processed: 52 average time/residue: 0.0757 time to fit residues: 6.0056 Evaluate side-chains 41 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1171 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.064642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.040000 restraints weight = 41409.972| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 4.18 r_work: 0.2728 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9514 Z= 0.230 Angle : 0.568 11.233 12934 Z= 0.285 Chirality : 0.045 0.475 1517 Planarity : 0.003 0.043 1628 Dihedral : 5.118 48.197 1348 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.62 % Allowed : 17.64 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.25), residues: 1160 helix: 1.60 (0.35), residues: 222 sheet: 0.78 (0.24), residues: 485 loop : -0.24 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.011 0.001 TYR A1002 PHE 0.012 0.001 PHE A 219 TRP 0.010 0.001 TRP A1124 HIS 0.003 0.001 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9508) covalent geometry : angle 0.55126 (12917) SS BOND : bond 0.00419 ( 1) SS BOND : angle 2.49539 ( 2) hydrogen bonds : bond 0.03047 ( 438) hydrogen bonds : angle 4.63693 ( 1236) link_NAG-ASN : bond 0.00657 ( 5) link_NAG-ASN : angle 3.92121 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 29 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.9031 (t0) cc_final: 0.8764 (t0) REVERT: A 125 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: A 875 SER cc_start: 0.8578 (OUTLIER) cc_final: 0.8351 (t) REVERT: A 1110 MET cc_start: 0.8944 (ppp) cc_final: 0.8537 (ppp) REVERT: A 1171 GLN cc_start: 0.9371 (OUTLIER) cc_final: 0.8982 (mm-40) outliers start: 38 outliers final: 28 residues processed: 66 average time/residue: 0.0736 time to fit residues: 7.6513 Evaluate side-chains 59 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 28 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 111 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.065482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041111 restraints weight = 40821.001| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.13 r_work: 0.2774 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9514 Z= 0.107 Angle : 0.499 10.721 12934 Z= 0.249 Chirality : 0.044 0.445 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.885 50.428 1348 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.48 % Allowed : 19.35 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.25), residues: 1160 helix: 1.75 (0.35), residues: 222 sheet: 0.78 (0.24), residues: 489 loop : -0.15 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 823 TYR 0.008 0.001 TYR A1002 PHE 0.011 0.001 PHE A 219 TRP 0.009 0.001 TRP A1124 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9508) covalent geometry : angle 0.48368 (12917) SS BOND : bond 0.00114 ( 1) SS BOND : angle 1.40787 ( 2) hydrogen bonds : bond 0.02668 ( 438) hydrogen bonds : angle 4.40705 ( 1236) link_NAG-ASN : bond 0.00588 ( 5) link_NAG-ASN : angle 3.60851 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASP cc_start: 0.8962 (t0) cc_final: 0.8761 (t0) REVERT: A 125 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: A 1110 MET cc_start: 0.8996 (ppp) cc_final: 0.8564 (ppp) outliers start: 26 outliers final: 19 residues processed: 54 average time/residue: 0.0713 time to fit residues: 6.2535 Evaluate side-chains 49 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 29 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 42 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 959 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.065053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.040716 restraints weight = 41272.584| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.12 r_work: 0.2760 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9514 Z= 0.148 Angle : 0.509 10.173 12934 Z= 0.254 Chirality : 0.044 0.414 1517 Planarity : 0.003 0.043 1628 Dihedral : 4.806 50.499 1348 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.96 % Allowed : 18.88 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.25), residues: 1160 helix: 1.83 (0.35), residues: 222 sheet: 0.80 (0.24), residues: 489 loop : -0.08 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 149 TYR 0.008 0.001 TYR A1002 PHE 0.012 0.001 PHE A 219 TRP 0.008 0.001 TRP A1124 HIS 0.001 0.000 HIS A1225 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9508) covalent geometry : angle 0.49535 (12917) SS BOND : bond 0.00588 ( 1) SS BOND : angle 1.95554 ( 2) hydrogen bonds : bond 0.02667 ( 438) hydrogen bonds : angle 4.40872 ( 1236) link_NAG-ASN : bond 0.00594 ( 5) link_NAG-ASN : angle 3.43631 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 29 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 794 MET cc_start: 0.8449 (tpp) cc_final: 0.8201 (tpp) REVERT: A 848 MET cc_start: 0.9076 (mmm) cc_final: 0.8822 (mmm) REVERT: A 1110 MET cc_start: 0.8948 (ppp) cc_final: 0.8524 (ppp) outliers start: 31 outliers final: 26 residues processed: 59 average time/residue: 0.0745 time to fit residues: 6.9348 Evaluate side-chains 56 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 29 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 71 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.065688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.041384 restraints weight = 40788.639| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 4.13 r_work: 0.2782 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9514 Z= 0.103 Angle : 0.502 9.960 12934 Z= 0.247 Chirality : 0.044 0.395 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.662 51.091 1348 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.67 % Allowed : 19.45 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.25), residues: 1160 helix: 1.99 (0.35), residues: 220 sheet: 0.86 (0.24), residues: 489 loop : -0.03 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 823 TYR 0.007 0.001 TYR A 534 PHE 0.011 0.001 PHE A 219 TRP 0.009 0.001 TRP A 639 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 9508) covalent geometry : angle 0.48910 (12917) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.23976 ( 2) hydrogen bonds : bond 0.02504 ( 438) hydrogen bonds : angle 4.26021 ( 1236) link_NAG-ASN : bond 0.00588 ( 5) link_NAG-ASN : angle 3.27396 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 29 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: A 794 MET cc_start: 0.8506 (tpp) cc_final: 0.8260 (tpp) REVERT: A 1110 MET cc_start: 0.8929 (ppp) cc_final: 0.8510 (ppp) REVERT: A 1171 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8588 (mp10) outliers start: 28 outliers final: 24 residues processed: 56 average time/residue: 0.0731 time to fit residues: 6.6463 Evaluate side-chains 55 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 29 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 13 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 101 optimal weight: 0.0770 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 83 optimal weight: 9.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 46 optimal weight: 0.0010 chunk 71 optimal weight: 4.9990 overall best weight: 0.9348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.065425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.041131 restraints weight = 40870.546| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.12 r_work: 0.2765 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9514 Z= 0.124 Angle : 0.509 9.778 12934 Z= 0.251 Chirality : 0.044 0.381 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.633 50.692 1348 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.96 % Allowed : 19.16 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.25), residues: 1160 helix: 1.96 (0.35), residues: 222 sheet: 0.88 (0.23), residues: 489 loop : 0.07 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 149 TYR 0.007 0.001 TYR A 617 PHE 0.011 0.001 PHE A 219 TRP 0.007 0.001 TRP A1124 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9508) covalent geometry : angle 0.49703 (12917) SS BOND : bond 0.00170 ( 1) SS BOND : angle 1.65939 ( 2) hydrogen bonds : bond 0.02537 ( 438) hydrogen bonds : angle 4.27203 ( 1236) link_NAG-ASN : bond 0.00590 ( 5) link_NAG-ASN : angle 3.19811 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 29 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: A 794 MET cc_start: 0.8494 (tpp) cc_final: 0.8228 (tpp) REVERT: A 848 MET cc_start: 0.9023 (mmm) cc_final: 0.8698 (mmm) REVERT: A 1110 MET cc_start: 0.8934 (ppp) cc_final: 0.8515 (ppp) outliers start: 31 outliers final: 27 residues processed: 59 average time/residue: 0.0772 time to fit residues: 7.3154 Evaluate side-chains 57 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 29 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 52 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.065794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.041544 restraints weight = 40655.511| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.12 r_work: 0.2783 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9514 Z= 0.102 Angle : 0.506 9.674 12934 Z= 0.248 Chirality : 0.044 0.374 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.549 51.279 1348 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.96 % Allowed : 19.07 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1160 helix: 2.00 (0.35), residues: 222 sheet: 0.95 (0.23), residues: 488 loop : 0.12 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 823 TYR 0.007 0.001 TYR A 534 PHE 0.011 0.001 PHE A 219 TRP 0.009 0.001 TRP A 639 HIS 0.001 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9508) covalent geometry : angle 0.49451 (12917) SS BOND : bond 0.00038 ( 1) SS BOND : angle 1.01807 ( 2) hydrogen bonds : bond 0.02463 ( 438) hydrogen bonds : angle 4.21069 ( 1236) link_NAG-ASN : bond 0.00590 ( 5) link_NAG-ASN : angle 3.11462 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 30 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: A 794 MET cc_start: 0.8500 (tpp) cc_final: 0.8220 (tpp) REVERT: A 848 MET cc_start: 0.9005 (mmm) cc_final: 0.8718 (mmm) REVERT: A 1110 MET cc_start: 0.8937 (ppp) cc_final: 0.8506 (ppp) REVERT: A 1143 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7762 (mm-30) REVERT: A 1171 GLN cc_start: 0.9346 (OUTLIER) cc_final: 0.8551 (mp10) outliers start: 31 outliers final: 28 residues processed: 60 average time/residue: 0.0828 time to fit residues: 7.9323 Evaluate side-chains 60 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 30 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1229 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.065532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041230 restraints weight = 40771.436| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 4.12 r_work: 0.2777 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9514 Z= 0.123 Angle : 0.553 12.322 12934 Z= 0.266 Chirality : 0.044 0.367 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.783 50.746 1348 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.86 % Allowed : 19.07 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.26), residues: 1160 helix: 2.03 (0.35), residues: 222 sheet: 0.95 (0.24), residues: 484 loop : 0.14 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 149 TYR 0.007 0.001 TYR A 356 PHE 0.011 0.001 PHE A 219 TRP 0.007 0.001 TRP A1124 HIS 0.002 0.000 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9508) covalent geometry : angle 0.52709 (12917) SS BOND : bond 0.00133 ( 1) SS BOND : angle 1.54074 ( 2) hydrogen bonds : bond 0.02527 ( 438) hydrogen bonds : angle 4.24000 ( 1236) link_NAG-ASN : bond 0.00834 ( 5) link_NAG-ASN : angle 4.91389 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2320 Ramachandran restraints generated. 1160 Oldfield, 0 Emsley, 1160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 30 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 794 MET cc_start: 0.8530 (tpp) cc_final: 0.8197 (tpp) REVERT: A 848 MET cc_start: 0.9026 (mmm) cc_final: 0.8729 (mmm) REVERT: A 1110 MET cc_start: 0.8945 (ppp) cc_final: 0.8519 (ppp) REVERT: A 1143 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7769 (mm-30) REVERT: A 1171 GLN cc_start: 0.9344 (OUTLIER) cc_final: 0.8540 (mp10) outliers start: 30 outliers final: 27 residues processed: 59 average time/residue: 0.0814 time to fit residues: 7.7492 Evaluate side-chains 59 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 30 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 393 VAL Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 706 TYR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 897 ILE Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 904 LEU Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1171 GLN Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1228 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 80 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1035 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.064980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.040513 restraints weight = 39705.032| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.04 r_work: 0.2726 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9514 Z= 0.169 Angle : 0.558 9.561 12934 Z= 0.273 Chirality : 0.044 0.354 1517 Planarity : 0.003 0.042 1628 Dihedral : 4.846 51.434 1348 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.96 % Allowed : 18.97 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.26), residues: 1160 helix: 2.02 (0.35), residues: 222 sheet: 0.90 (0.24), residues: 487 loop : 0.13 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 149 TYR 0.009 0.001 TYR A1147 PHE 0.012 0.001 PHE A 219 TRP 0.007 0.001 TRP A1124 HIS 0.002 0.001 HIS A 689 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9508) covalent geometry : angle 0.54381 (12917) SS BOND : bond 0.00266 ( 1) SS BOND : angle 1.80227 ( 2) hydrogen bonds : bond 0.02751 ( 438) hydrogen bonds : angle 4.40460 ( 1236) link_NAG-ASN : bond 0.00671 ( 5) link_NAG-ASN : angle 3.64872 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.35 seconds wall clock time: 41 minutes 1.37 seconds (2461.37 seconds total)