Starting phenix.real_space_refine on Fri Aug 22 14:53:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jle_36394/08_2025/8jle_36394.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.038 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 15 5.16 5 C 2819 2.51 5 N 735 2.21 5 O 839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s 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: 4408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 905 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "B" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3437 Classifications: {'peptide': 420} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.23, per 1000 atoms: 0.28 Number of scatterers: 4408 At special positions: 0 Unit cell: (88.81, 83.83, 87.98, 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 15 16.00 O 839 8.00 N 735 7.00 C 2819 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Atom "HETATM 4406 O5 NAG A 602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG E 1 " - " FUC E 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 498 " " NAG A 602 " - " ASN A 548 " " NAG E 1 " - " ASN A 573 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 99.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 10 sheets defined 7.8% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 562 through 564 No H-bonds generated for 'chain 'A' and resid 562 through 564' Processing helix chain 'B' and resid 929 through 933 removed outlier: 3.759A pdb=" N VAL B 933 " --> pdb=" O ASN B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 958 Processing helix chain 'B' and resid 1080 through 1092 Processing helix chain 'B' and resid 1210 through 1215 removed outlier: 3.812A pdb=" N VAL B1214 " --> pdb=" O ILE B1211 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY B1215 " --> pdb=" O PRO B1212 " (cutoff:3.500A) Processing helix chain 'B' and resid 1265 through 1273 Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492 removed outlier: 6.248A pdb=" N GLY A 509 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG A 491 " --> pdb=" O GLY A 509 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A 511 " --> pdb=" O ARG A 491 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR A 500 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 523 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 515 through 527 current: chain 'A' and resid 550 through 552 removed outlier: 6.220A pdb=" N PHE A 551 " --> pdb=" O ILE A 572 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567 removed outlier: 6.085A pdb=" N PHE A 546 " --> pdb=" O VAL A 567 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE A 545 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N THR A 500 " --> pdb=" O LEU A 521 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N SER A 523 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU A 502 " --> pdb=" O SER A 523 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N SER A 525 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN A 504 " --> pdb=" O SER A 525 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU A 527 " --> pdb=" O GLN A 504 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N HIS A 506 " --> pdb=" O GLU A 527 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 512 current: chain 'A' and resid 555 through 559 Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.588A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.520A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.204A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890 removed outlier: 3.588A pdb=" N ASP B 887 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B1074 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 880 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N PHE B1072 " --> pdb=" O SER B 880 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL B 882 " --> pdb=" O LYS B1070 " (cutoff:3.500A) removed outlier: 10.872A pdb=" N LYS B1070 " --> pdb=" O VAL B 882 " (cutoff:3.500A) removed outlier: 16.520A pdb=" N LYS B 884 " --> pdb=" O MET B1068 " (cutoff:3.500A) removed outlier: 18.204A pdb=" N MET B1068 " --> pdb=" O LYS B 884 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B1072 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER B 944 " --> pdb=" O PHE B1072 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B1074 " --> pdb=" O SER B 942 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER B 942 " --> pdb=" O LEU B1074 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B1037 " --> pdb=" O ILE B1029 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE B1031 " --> pdb=" O LEU B1035 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU B1035 " --> pdb=" O ILE B1031 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900 Processing sheet with id=AA6, first strand: chain 'B' and resid 962 through 966 removed outlier: 6.682A pdb=" N VAL B 976 " --> pdb=" O ILE B 964 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN B 966 " --> pdb=" O TRP B 974 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP B 974 " --> pdb=" O ASN B 966 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1115 Processing sheet with id=AA8, first strand: chain 'B' and resid 1122 through 1125 Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.100A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B1220 " --> pdb=" O GLN B1240 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LYS B1226 " --> pdb=" O LYS B1234 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LYS B1234 " --> pdb=" O LYS B1226 " (cutoff:3.500A) removed outlier: 27.490A pdb=" N ASN B1233 " --> pdb=" O LEU B1254 " (cutoff:3.500A) removed outlier: 23.639A pdb=" N LEU B1254 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 16.033A pdb=" N CYS B1235 " --> pdb=" O PHE B1252 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N PHE B1252 " --> pdb=" O CYS B1235 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N MET B1237 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B1204 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164 removed outlier: 4.100A pdb=" N LYS B1159 " --> pdb=" O VAL B1185 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE B1182 " --> pdb=" O LEU B1193 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 348 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: 0.70 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 734 1.31 - 1.46: 1688 1.46 - 1.60: 2056 1.60 - 1.74: 0 1.74 - 1.88: 23 Bond restraints: 4501 Sorted by residual: bond pdb=" C ILE B1182 " pdb=" O ILE B1182 " ideal model delta sigma weight residual 1.238 1.172 0.066 1.10e-02 8.26e+03 3.55e+01 bond pdb=" C TYR B1001 " pdb=" O TYR B1001 " ideal model delta sigma weight residual 1.235 1.189 0.046 1.14e-02 7.69e+03 1.65e+01 bond pdb=" C LYS A 515 " pdb=" O LYS A 515 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" C MET B1134 " pdb=" O MET B1134 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.22e-02 6.72e+03 1.51e+01 bond pdb=" CA SER B1281 " pdb=" CB SER B1281 " ideal model delta sigma weight residual 1.532 1.474 0.058 1.58e-02 4.01e+03 1.36e+01 ... (remaining 4496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 4819 1.37 - 2.75: 1031 2.75 - 4.12: 197 4.12 - 5.49: 27 5.49 - 6.86: 7 Bond angle restraints: 6081 Sorted by residual: angle pdb=" OD1 ASN A 498 " pdb=" CG ASN A 498 " pdb=" ND2 ASN A 498 " ideal model delta sigma weight residual 122.60 116.40 6.20 1.00e+00 1.00e+00 3.84e+01 angle pdb=" OD1 ASN A 573 " pdb=" CG ASN A 573 " pdb=" ND2 ASN A 573 " ideal model delta sigma weight residual 122.60 118.39 4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" CA GLY B1141 " pdb=" C GLY B1141 " pdb=" O GLY B1141 " ideal model delta sigma weight residual 122.47 118.79 3.68 1.08e+00 8.57e-01 1.16e+01 angle pdb=" CA TYR B1107 " pdb=" C TYR B1107 " pdb=" O TYR B1107 " ideal model delta sigma weight residual 121.47 117.66 3.81 1.15e+00 7.56e-01 1.10e+01 angle pdb=" NH1 ARG A 547 " pdb=" CZ ARG A 547 " pdb=" NH2 ARG A 547 " ideal model delta sigma weight residual 119.30 123.55 -4.25 1.30e+00 5.92e-01 1.07e+01 ... (remaining 6076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 2469 14.90 - 29.81: 202 29.81 - 44.71: 52 44.71 - 59.62: 7 59.62 - 74.52: 6 Dihedral angle restraints: 2736 sinusoidal: 1180 harmonic: 1556 Sorted by residual: dihedral pdb=" CA ILE B1053 " pdb=" C ILE B1053 " pdb=" N MET B1054 " pdb=" CA MET B1054 " ideal model delta harmonic sigma weight residual 180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA ASP B1246 " pdb=" C ASP B1246 " pdb=" N ILE B1247 " pdb=" CA ILE B1247 " ideal model delta harmonic sigma weight residual 180.00 162.36 17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS B1204 " pdb=" C LYS B1204 " pdb=" N ILE B1205 " pdb=" CA ILE B1205 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 2733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.223: 663 0.223 - 0.447: 5 0.447 - 0.670: 1 0.670 - 0.894: 0 0.894 - 1.117: 1 Chirality restraints: 670 Sorted by residual: chirality pdb=" C1 FUC E 3 " pdb=" O6 NAG E 1 " pdb=" C2 FUC E 3 " pdb=" O5 FUC E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.09e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 498 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.59e+01 ... (remaining 667 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 573 " 0.052 2.00e-02 2.50e+03 5.90e-02 4.35e+01 pdb=" CG ASN A 573 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 573 " -0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 573 " -0.096 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.057 2.00e-02 2.50e+03 4.73e-02 2.79e+01 pdb=" C7 NAG A 602 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1014 " -0.061 2.00e-02 2.50e+03 3.28e-02 2.69e+01 pdb=" CG TRP B1014 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B1014 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B1014 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B1014 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TRP B1014 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1014 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1014 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1014 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP B1014 " -0.017 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 399 2.74 - 3.28: 4285 3.28 - 3.82: 7135 3.82 - 4.36: 9175 4.36 - 4.90: 15367 Nonbonded interactions: 36361 Sorted by model distance: nonbonded pdb=" OG1 THR B1195 " pdb=" O ILE B1205 " model vdw 2.204 3.040 nonbonded pdb=" O TRP B1266 " pdb=" NE2 GLN B1270 " model vdw 2.208 3.120 nonbonded pdb=" O GLU B1203 " pdb=" OH TYR B1255 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR A 484 " pdb=" OD1 ASN A 503 " model vdw 2.291 3.040 nonbonded pdb=" NH1 ARG A 507 " pdb=" OE1 GLU A 527 " model vdw 2.295 3.120 ... (remaining 36356 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.750 Find NCS groups from input model: 0.010 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.011 0.244 4506 Z= 0.655 Angle : 1.434 37.593 6096 Z= 0.802 Chirality : 0.096 1.117 670 Planarity : 0.010 0.090 772 Dihedral : 12.340 74.519 1740 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.34 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.99 (0.36), residues: 524 helix: 2.06 (1.09), residues: 23 sheet: -0.20 (0.33), residues: 244 loop : -1.35 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.003 ARG B1140 TYR 0.051 0.011 TYR B1111 PHE 0.057 0.012 PHE A 576 TRP 0.061 0.015 TRP B1014 HIS 0.008 0.004 HIS B1253 Details of bonding type rmsd covalent geometry : bond 0.01016 ( 4501) covalent geometry : angle 1.21278 ( 6081) hydrogen bonds : bond 0.14619 ( 129) hydrogen bonds : angle 7.34636 ( 348) link_BETA1-4 : bond 0.00356 ( 1) link_BETA1-4 : angle 2.13689 ( 3) link_BETA1-6 : bond 0.01819 ( 1) link_BETA1-6 : angle 2.18119 ( 3) link_NAG-ASN : bond 0.19294 ( 3) link_NAG-ASN : angle 19.89515 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 513 ASN cc_start: 0.7366 (t0) cc_final: 0.7130 (t0) REVERT: A 532 GLU cc_start: 0.7623 (tt0) cc_final: 0.6899 (tm-30) REVERT: A 572 ILE cc_start: 0.7827 (mt) cc_final: 0.7616 (mt) REVERT: B 913 GLN cc_start: 0.7056 (pt0) cc_final: 0.6828 (pt0) REVERT: B 940 ASN cc_start: 0.5482 (m-40) cc_final: 0.5168 (m-40) REVERT: B 955 LYS cc_start: 0.7396 (pptt) cc_final: 0.7174 (pttt) REVERT: B 982 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 988 GLN cc_start: 0.7010 (tt0) cc_final: 0.6779 (tt0) REVERT: B 1000 LYS cc_start: 0.8190 (tptp) cc_final: 0.7745 (mttp) REVERT: B 1083 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6721 (mt-10) REVERT: B 1085 LYS cc_start: 0.6078 (tptm) cc_final: 0.5806 (mmtt) REVERT: B 1089 ASP cc_start: 0.6994 (m-30) cc_final: 0.6718 (m-30) REVERT: B 1106 GLN cc_start: 0.7631 (mt0) cc_final: 0.7375 (mt0) REVERT: B 1117 PHE cc_start: 0.6115 (m-10) cc_final: 0.5286 (t80) REVERT: B 1158 THR cc_start: 0.8314 (m) cc_final: 0.8043 (p) REVERT: B 1165 TYR cc_start: 0.5874 (t80) cc_final: 0.5477 (t80) REVERT: B 1173 ILE cc_start: 0.7717 (mt) cc_final: 0.7415 (mp) REVERT: B 1179 ARG cc_start: 0.6833 (mtt180) cc_final: 0.5966 (mtp-110) REVERT: B 1189 LYS cc_start: 0.6324 (tppt) cc_final: 0.5843 (mtpm) REVERT: B 1206 LEU cc_start: 0.7066 (mp) cc_final: 0.6862 (mt) REVERT: B 1237 MET cc_start: 0.8903 (mtm) cc_final: 0.8499 (mtm) REVERT: B 1246 ASP cc_start: 0.7648 (p0) cc_final: 0.7181 (m-30) REVERT: B 1256 ASP cc_start: 0.7481 (m-30) cc_final: 0.7003 (p0) REVERT: B 1265 ASN cc_start: 0.7146 (m-40) cc_final: 0.6883 (m-40) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.4450 time to fit residues: 62.8870 Evaluate side-chains 93 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 970 ASN B 992 GLN B1091 GLN B1093 ASN B1257 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136835 restraints weight = 4977.078| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.34 r_work: 0.3338 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4506 Z= 0.160 Angle : 0.659 11.827 6096 Z= 0.341 Chirality : 0.056 0.575 670 Planarity : 0.004 0.030 772 Dihedral : 7.274 59.912 684 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.88 % Allowed : 11.11 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 524 helix: 2.34 (1.07), residues: 23 sheet: -0.22 (0.32), residues: 259 loop : -1.07 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1192 TYR 0.011 0.002 TYR B1104 PHE 0.018 0.002 PHE A 516 TRP 0.018 0.002 TRP B1266 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4501) covalent geometry : angle 0.61860 ( 6081) hydrogen bonds : bond 0.03543 ( 129) hydrogen bonds : angle 5.97987 ( 348) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 1.51378 ( 3) link_BETA1-6 : bond 0.00393 ( 1) link_BETA1-6 : angle 1.34809 ( 3) link_NAG-ASN : bond 0.01191 ( 3) link_NAG-ASN : angle 5.83483 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.190 Fit side-chains REVERT: A 532 GLU cc_start: 0.8215 (tt0) cc_final: 0.7662 (tm-30) REVERT: A 581 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: B 982 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 988 GLN cc_start: 0.7887 (tt0) cc_final: 0.7571 (tt0) REVERT: B 993 ASN cc_start: 0.7119 (m110) cc_final: 0.6813 (m110) REVERT: B 1037 ASP cc_start: 0.8533 (t0) cc_final: 0.8195 (t0) REVERT: B 1058 ASP cc_start: 0.7106 (t70) cc_final: 0.6765 (t0) REVERT: B 1083 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7609 (mt-10) REVERT: B 1085 LYS cc_start: 0.7174 (tptm) cc_final: 0.6877 (mmtt) REVERT: B 1089 ASP cc_start: 0.7643 (m-30) cc_final: 0.7295 (m-30) REVERT: B 1117 PHE cc_start: 0.6622 (m-10) cc_final: 0.6110 (t80) REVERT: B 1173 ILE cc_start: 0.8603 (mt) cc_final: 0.8317 (mp) REVERT: B 1179 ARG cc_start: 0.7631 (mtt180) cc_final: 0.7199 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7477 (tppt) cc_final: 0.7003 (mtpm) REVERT: B 1237 MET cc_start: 0.8774 (mtm) cc_final: 0.8515 (mtm) outliers start: 14 outliers final: 5 residues processed: 108 average time/residue: 0.5074 time to fit residues: 56.9459 Evaluate side-chains 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 ASN B 940 ASN ** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 966 ASN B 970 ASN B 992 GLN B1093 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.170672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127055 restraints weight = 4936.572| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.34 r_work: 0.3208 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4506 Z= 0.269 Angle : 0.747 11.704 6096 Z= 0.390 Chirality : 0.061 0.586 670 Planarity : 0.005 0.056 772 Dihedral : 6.495 51.334 684 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.14 % Allowed : 13.58 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.00 (0.35), residues: 524 helix: -0.04 (1.00), residues: 29 sheet: -0.09 (0.39), residues: 165 loop : -1.04 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 570 TYR 0.019 0.002 TYR B 938 PHE 0.020 0.002 PHE A 516 TRP 0.021 0.003 TRP B1266 HIS 0.004 0.002 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00658 ( 4501) covalent geometry : angle 0.71528 ( 6081) hydrogen bonds : bond 0.03987 ( 129) hydrogen bonds : angle 6.14965 ( 348) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 1.66234 ( 3) link_BETA1-6 : bond 0.00207 ( 1) link_BETA1-6 : angle 1.49512 ( 3) link_NAG-ASN : bond 0.00770 ( 3) link_NAG-ASN : angle 5.56755 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.174 Fit side-chains REVERT: A 532 GLU cc_start: 0.8325 (tt0) cc_final: 0.7724 (tm-30) REVERT: A 533 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 903 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7422 (mmm160) REVERT: B 988 GLN cc_start: 0.8023 (tt0) cc_final: 0.7717 (tt0) REVERT: B 1000 LYS cc_start: 0.8822 (mttp) cc_final: 0.8614 (mttp) REVERT: B 1037 ASP cc_start: 0.8543 (t0) cc_final: 0.8235 (t70) REVERT: B 1054 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: B 1058 ASP cc_start: 0.7473 (t70) cc_final: 0.7040 (t0) REVERT: B 1064 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7744 (mtp180) REVERT: B 1083 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7681 (mt-10) REVERT: B 1085 LYS cc_start: 0.7331 (tptm) cc_final: 0.7046 (mmtt) REVERT: B 1117 PHE cc_start: 0.7517 (m-10) cc_final: 0.6817 (t80) REVERT: B 1179 ARG cc_start: 0.7923 (mtt180) cc_final: 0.7400 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7609 (tppt) cc_final: 0.7054 (mtpm) outliers start: 25 outliers final: 9 residues processed: 113 average time/residue: 0.4615 time to fit residues: 54.2582 Evaluate side-chains 100 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 516 PHE Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 977 SER Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1054 MET Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 960 ASN B 970 ASN B 992 GLN B1093 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.173685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.130352 restraints weight = 4919.773| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.33 r_work: 0.3233 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4506 Z= 0.145 Angle : 0.588 8.732 6096 Z= 0.312 Chirality : 0.054 0.497 670 Planarity : 0.003 0.034 772 Dihedral : 5.956 51.511 684 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.73 % Allowed : 15.84 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.36), residues: 524 helix: 0.06 (1.01), residues: 29 sheet: 0.03 (0.40), residues: 168 loop : -0.87 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 570 TYR 0.021 0.002 TYR B1181 PHE 0.017 0.001 PHE A 516 TRP 0.018 0.002 TRP B1266 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4501) covalent geometry : angle 0.56412 ( 6081) hydrogen bonds : bond 0.03101 ( 129) hydrogen bonds : angle 5.80911 ( 348) link_BETA1-4 : bond 0.00727 ( 1) link_BETA1-4 : angle 0.90165 ( 3) link_BETA1-6 : bond 0.00541 ( 1) link_BETA1-6 : angle 1.31203 ( 3) link_NAG-ASN : bond 0.00620 ( 3) link_NAG-ASN : angle 4.23706 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.207 Fit side-chains REVERT: A 513 ASN cc_start: 0.8383 (t0) cc_final: 0.8127 (m-40) REVERT: A 532 GLU cc_start: 0.8312 (tt0) cc_final: 0.7723 (tm-30) REVERT: A 581 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: B 988 GLN cc_start: 0.8021 (tt0) cc_final: 0.7720 (tt0) REVERT: B 1037 ASP cc_start: 0.8488 (t0) cc_final: 0.8164 (t70) REVERT: B 1052 LYS cc_start: 0.7609 (ptpp) cc_final: 0.7130 (ptpt) REVERT: B 1058 ASP cc_start: 0.7428 (t70) cc_final: 0.6985 (t0) REVERT: B 1085 LYS cc_start: 0.7338 (tptm) cc_final: 0.7060 (mmtt) REVERT: B 1117 PHE cc_start: 0.7370 (m-10) cc_final: 0.6673 (t80) REVERT: B 1179 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7346 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7645 (tppt) cc_final: 0.7046 (mtpm) REVERT: B 1203 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6956 (mt-10) REVERT: B 1210 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7541 (mp0) outliers start: 23 outliers final: 11 residues processed: 95 average time/residue: 0.4828 time to fit residues: 47.7454 Evaluate side-chains 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1210 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B 992 GLN B1003 GLN B1093 ASN B1115 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1233 ASN B1270 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.172306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133964 restraints weight = 4946.748| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.13 r_work: 0.3233 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4506 Z= 0.182 Angle : 0.593 8.218 6096 Z= 0.317 Chirality : 0.054 0.470 670 Planarity : 0.003 0.027 772 Dihedral : 5.792 49.152 684 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.94 % Allowed : 17.70 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.71 (0.36), residues: 524 helix: 1.41 (1.06), residues: 23 sheet: 0.10 (0.41), residues: 159 loop : -0.91 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.017 0.002 TYR B1133 PHE 0.016 0.002 PHE A 516 TRP 0.012 0.002 TRP B1266 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 4501) covalent geometry : angle 0.57189 ( 6081) hydrogen bonds : bond 0.03210 ( 129) hydrogen bonds : angle 5.82891 ( 348) link_BETA1-4 : bond 0.00602 ( 1) link_BETA1-4 : angle 1.11425 ( 3) link_BETA1-6 : bond 0.00272 ( 1) link_BETA1-6 : angle 1.31911 ( 3) link_NAG-ASN : bond 0.00571 ( 3) link_NAG-ASN : angle 4.02346 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.203 Fit side-chains REVERT: A 513 ASN cc_start: 0.8413 (t0) cc_final: 0.8170 (m-40) REVERT: A 532 GLU cc_start: 0.8242 (tt0) cc_final: 0.7642 (tm-30) REVERT: B 903 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7441 (mmm160) REVERT: B 988 GLN cc_start: 0.8032 (tt0) cc_final: 0.7736 (tt0) REVERT: B 1037 ASP cc_start: 0.8481 (t0) cc_final: 0.8082 (t70) REVERT: B 1052 LYS cc_start: 0.7693 (ptpp) cc_final: 0.6841 (ptpp) REVERT: B 1058 ASP cc_start: 0.7397 (t70) cc_final: 0.6920 (t0) REVERT: B 1085 LYS cc_start: 0.7260 (tptm) cc_final: 0.6982 (mmtt) REVERT: B 1117 PHE cc_start: 0.7376 (m-10) cc_final: 0.6862 (t80) REVERT: B 1179 ARG cc_start: 0.7828 (mtt180) cc_final: 0.7330 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7637 (tppt) cc_final: 0.7014 (mtpm) outliers start: 24 outliers final: 13 residues processed: 98 average time/residue: 0.4810 time to fit residues: 48.9856 Evaluate side-chains 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B 992 GLN B1003 GLN B1093 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.173565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134611 restraints weight = 5031.517| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.23 r_work: 0.3281 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4506 Z= 0.117 Angle : 0.526 5.870 6096 Z= 0.286 Chirality : 0.051 0.386 670 Planarity : 0.003 0.032 772 Dihedral : 5.456 46.825 684 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.70 % Allowed : 19.14 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.46 (0.37), residues: 524 helix: 1.41 (1.10), residues: 23 sheet: 0.25 (0.41), residues: 158 loop : -0.71 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B1192 TYR 0.015 0.001 TYR B1133 PHE 0.015 0.001 PHE A 516 TRP 0.010 0.001 TRP B 985 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4501) covalent geometry : angle 0.51015 ( 6081) hydrogen bonds : bond 0.02805 ( 129) hydrogen bonds : angle 5.58161 ( 348) link_BETA1-4 : bond 0.00650 ( 1) link_BETA1-4 : angle 0.95376 ( 3) link_BETA1-6 : bond 0.00453 ( 1) link_BETA1-6 : angle 1.21661 ( 3) link_NAG-ASN : bond 0.00668 ( 3) link_NAG-ASN : angle 3.25965 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.125 Fit side-chains REVERT: A 532 GLU cc_start: 0.8281 (tt0) cc_final: 0.7702 (tm-30) REVERT: B 903 ARG cc_start: 0.7674 (mmm160) cc_final: 0.7473 (mmm160) REVERT: B 988 GLN cc_start: 0.8014 (tt0) cc_final: 0.7742 (tt0) REVERT: B 1004 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.7583 (mpt) REVERT: B 1037 ASP cc_start: 0.8512 (t0) cc_final: 0.8067 (t70) REVERT: B 1052 LYS cc_start: 0.7691 (ptpp) cc_final: 0.7252 (ptmt) REVERT: B 1058 ASP cc_start: 0.7398 (t70) cc_final: 0.6901 (t0) REVERT: B 1083 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7538 (mt-10) REVERT: B 1085 LYS cc_start: 0.7273 (tptm) cc_final: 0.7007 (mmtt) REVERT: B 1117 PHE cc_start: 0.7362 (m-10) cc_final: 0.6865 (t80) REVERT: B 1179 ARG cc_start: 0.7801 (mtt180) cc_final: 0.7242 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7613 (tppt) cc_final: 0.7014 (mtpm) REVERT: B 1253 HIS cc_start: 0.8183 (t-170) cc_final: 0.7953 (t70) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.4427 time to fit residues: 44.1477 Evaluate side-chains 92 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B1003 GLN B1093 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.171151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127666 restraints weight = 5009.208| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.35 r_work: 0.3299 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4506 Z= 0.165 Angle : 0.572 6.484 6096 Z= 0.307 Chirality : 0.053 0.407 670 Planarity : 0.003 0.025 772 Dihedral : 5.503 44.764 684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.32 % Allowed : 19.14 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.37), residues: 524 helix: 1.42 (1.11), residues: 23 sheet: 0.26 (0.44), residues: 147 loop : -0.67 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.016 0.002 TYR B1133 PHE 0.016 0.002 PHE A 516 TRP 0.010 0.001 TRP B 974 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4501) covalent geometry : angle 0.55479 ( 6081) hydrogen bonds : bond 0.03020 ( 129) hydrogen bonds : angle 5.64369 ( 348) link_BETA1-4 : bond 0.00540 ( 1) link_BETA1-4 : angle 1.11292 ( 3) link_BETA1-6 : bond 0.00410 ( 1) link_BETA1-6 : angle 1.33655 ( 3) link_NAG-ASN : bond 0.00542 ( 3) link_NAG-ASN : angle 3.50528 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.135 Fit side-chains REVERT: A 513 ASN cc_start: 0.8650 (m-40) cc_final: 0.8413 (m-40) REVERT: A 532 GLU cc_start: 0.8330 (tt0) cc_final: 0.7791 (tm-30) REVERT: A 533 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8508 (mm-30) REVERT: B 903 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7453 (mmm160) REVERT: B 971 ASN cc_start: 0.7968 (m110) cc_final: 0.7542 (m110) REVERT: B 988 GLN cc_start: 0.8031 (tt0) cc_final: 0.7787 (tt0) REVERT: B 1004 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.7484 (mpt) REVERT: B 1037 ASP cc_start: 0.8506 (t0) cc_final: 0.8160 (t70) REVERT: B 1052 LYS cc_start: 0.7699 (ptpp) cc_final: 0.7251 (ptmt) REVERT: B 1058 ASP cc_start: 0.7481 (t70) cc_final: 0.6965 (t0) REVERT: B 1085 LYS cc_start: 0.7320 (tptm) cc_final: 0.7042 (mmtt) REVERT: B 1117 PHE cc_start: 0.7396 (m-10) cc_final: 0.6931 (t80) REVERT: B 1179 ARG cc_start: 0.7824 (mtt180) cc_final: 0.7290 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7678 (tppt) cc_final: 0.7064 (mtpm) outliers start: 21 outliers final: 13 residues processed: 99 average time/residue: 0.4122 time to fit residues: 42.5008 Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B 992 GLN B1003 GLN B1093 ASN ** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.170834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.131843 restraints weight = 5013.595| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.22 r_work: 0.3256 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4506 Z= 0.150 Angle : 0.561 5.997 6096 Z= 0.302 Chirality : 0.052 0.387 670 Planarity : 0.003 0.031 772 Dihedral : 5.421 44.985 684 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.50 % Allowed : 19.96 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.41 (0.37), residues: 524 helix: 1.38 (1.14), residues: 23 sheet: 0.25 (0.44), residues: 147 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.017 0.001 TYR B1133 PHE 0.015 0.001 PHE A 516 TRP 0.009 0.001 TRP B 985 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4501) covalent geometry : angle 0.54552 ( 6081) hydrogen bonds : bond 0.02909 ( 129) hydrogen bonds : angle 5.59320 ( 348) link_BETA1-4 : bond 0.00659 ( 1) link_BETA1-4 : angle 1.00585 ( 3) link_BETA1-6 : bond 0.00393 ( 1) link_BETA1-6 : angle 1.30019 ( 3) link_NAG-ASN : bond 0.00578 ( 3) link_NAG-ASN : angle 3.35166 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.122 Fit side-chains REVERT: A 532 GLU cc_start: 0.8309 (tt0) cc_final: 0.7753 (tm-30) REVERT: B 903 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7437 (mmm160) REVERT: B 971 ASN cc_start: 0.7935 (m110) cc_final: 0.7491 (m110) REVERT: B 988 GLN cc_start: 0.8034 (tt0) cc_final: 0.7736 (tt0) REVERT: B 1004 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.7447 (mpt) REVERT: B 1037 ASP cc_start: 0.8512 (t0) cc_final: 0.8157 (t70) REVERT: B 1052 LYS cc_start: 0.7675 (ptpp) cc_final: 0.6859 (ptpp) REVERT: B 1058 ASP cc_start: 0.7446 (t70) cc_final: 0.6931 (t0) REVERT: B 1085 LYS cc_start: 0.7247 (tptm) cc_final: 0.6967 (mmtt) REVERT: B 1117 PHE cc_start: 0.7374 (m-10) cc_final: 0.6911 (t80) REVERT: B 1179 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7238 (mtm-85) REVERT: B 1189 LYS cc_start: 0.7677 (tppt) cc_final: 0.7049 (mtpm) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.4395 time to fit residues: 43.0160 Evaluate side-chains 98 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1218 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 970 ASN B 992 GLN B1003 GLN B1093 ASN B1199 GLN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.170040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131380 restraints weight = 5001.180| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.15 r_work: 0.3262 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4506 Z= 0.152 Angle : 0.563 5.939 6096 Z= 0.304 Chirality : 0.052 0.385 670 Planarity : 0.003 0.025 772 Dihedral : 5.455 44.339 684 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.32 % Allowed : 19.34 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.40 (0.37), residues: 524 helix: 1.24 (1.16), residues: 23 sheet: 0.23 (0.43), residues: 149 loop : -0.58 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.016 0.001 TYR B1133 PHE 0.020 0.001 PHE A 512 TRP 0.010 0.001 TRP B 974 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 4501) covalent geometry : angle 0.54777 ( 6081) hydrogen bonds : bond 0.02870 ( 129) hydrogen bonds : angle 5.50475 ( 348) link_BETA1-4 : bond 0.00630 ( 1) link_BETA1-4 : angle 0.99011 ( 3) link_BETA1-6 : bond 0.00385 ( 1) link_BETA1-6 : angle 1.31546 ( 3) link_NAG-ASN : bond 0.00560 ( 3) link_NAG-ASN : angle 3.35959 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.177 Fit side-chains REVERT: A 532 GLU cc_start: 0.8313 (tt0) cc_final: 0.7777 (tm-30) REVERT: B 903 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7417 (mmm160) REVERT: B 971 ASN cc_start: 0.7894 (m110) cc_final: 0.7488 (m110) REVERT: B 988 GLN cc_start: 0.8026 (tt0) cc_final: 0.7775 (tt0) REVERT: B 1004 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7431 (mpt) REVERT: B 1037 ASP cc_start: 0.8490 (t0) cc_final: 0.8134 (t70) REVERT: B 1052 LYS cc_start: 0.7691 (ptpp) cc_final: 0.7292 (ptpt) REVERT: B 1058 ASP cc_start: 0.7425 (t70) cc_final: 0.6911 (t0) REVERT: B 1085 LYS cc_start: 0.7255 (tptm) cc_final: 0.6987 (mmtt) REVERT: B 1117 PHE cc_start: 0.7436 (m-10) cc_final: 0.6962 (t80) REVERT: B 1189 LYS cc_start: 0.7719 (tppt) cc_final: 0.7105 (mtpm) REVERT: B 1253 HIS cc_start: 0.8256 (t-90) cc_final: 0.7967 (t70) outliers start: 21 outliers final: 16 residues processed: 96 average time/residue: 0.4491 time to fit residues: 44.7648 Evaluate side-chains 96 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 970 ASN B 992 GLN B1003 GLN B1093 ASN B1199 GLN ** B1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1257 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.167739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.128677 restraints weight = 5047.834| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.18 r_work: 0.3243 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4506 Z= 0.166 Angle : 0.577 6.089 6096 Z= 0.312 Chirality : 0.053 0.392 670 Planarity : 0.003 0.032 772 Dihedral : 5.497 44.196 684 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.91 % Allowed : 19.96 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.40 (0.37), residues: 524 helix: 1.18 (1.17), residues: 23 sheet: 0.30 (0.43), residues: 154 loop : -0.64 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1175 TYR 0.020 0.001 TYR B1133 PHE 0.022 0.002 PHE A 512 TRP 0.010 0.001 TRP B 974 HIS 0.003 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 4501) covalent geometry : angle 0.56135 ( 6081) hydrogen bonds : bond 0.02984 ( 129) hydrogen bonds : angle 5.61843 ( 348) link_BETA1-4 : bond 0.00565 ( 1) link_BETA1-4 : angle 1.01296 ( 3) link_BETA1-6 : bond 0.00231 ( 1) link_BETA1-6 : angle 1.30004 ( 3) link_NAG-ASN : bond 0.00526 ( 3) link_NAG-ASN : angle 3.45707 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1048 Ramachandran restraints generated. 524 Oldfield, 0 Emsley, 524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 532 GLU cc_start: 0.8308 (tt0) cc_final: 0.7781 (tm-30) REVERT: B 971 ASN cc_start: 0.7889 (m110) cc_final: 0.7461 (m110) REVERT: B 988 GLN cc_start: 0.8017 (tt0) cc_final: 0.7725 (tt0) REVERT: B 1004 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7503 (mpt) REVERT: B 1037 ASP cc_start: 0.8501 (t0) cc_final: 0.8147 (t70) REVERT: B 1052 LYS cc_start: 0.7671 (ptpp) cc_final: 0.6861 (ptpp) REVERT: B 1058 ASP cc_start: 0.7414 (t70) cc_final: 0.6942 (t0) REVERT: B 1085 LYS cc_start: 0.7255 (tptm) cc_final: 0.7000 (mmtt) REVERT: B 1117 PHE cc_start: 0.7455 (m-10) cc_final: 0.7024 (t80) REVERT: B 1189 LYS cc_start: 0.7741 (tppt) cc_final: 0.7120 (mtpm) REVERT: B 1253 HIS cc_start: 0.8325 (t-90) cc_final: 0.8034 (t70) outliers start: 19 outliers final: 16 residues processed: 93 average time/residue: 0.4631 time to fit residues: 44.7457 Evaluate side-chains 95 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain B residue 908 SER Chi-restraints excluded: chain B residue 937 MET Chi-restraints excluded: chain B residue 943 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain B residue 1018 THR Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1050 SER Chi-restraints excluded: chain B residue 1064 ARG Chi-restraints excluded: chain B residue 1069 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1143 VAL Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1164 LYS Chi-restraints excluded: chain B residue 1204 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 49 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN B 970 ASN B 992 GLN B1003 GLN B1093 ASN B1199 GLN B1257 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.132286 restraints weight = 5032.713| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.20 r_work: 0.3288 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4506 Z= 0.118 Angle : 0.542 6.146 6096 Z= 0.294 Chirality : 0.051 0.353 670 Planarity : 0.003 0.030 772 Dihedral : 5.361 44.098 684 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.70 % Allowed : 19.75 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.31 (0.37), residues: 524 helix: 1.23 (1.16), residues: 23 sheet: 0.32 (0.44), residues: 147 loop : -0.52 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1175 TYR 0.017 0.001 TYR B1133 PHE 0.027 0.001 PHE A 512 TRP 0.009 0.001 TRP B 985 HIS 0.002 0.001 HIS A 494 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 4501) covalent geometry : angle 0.52806 ( 6081) hydrogen bonds : bond 0.02701 ( 129) hydrogen bonds : angle 5.43931 ( 348) link_BETA1-4 : bond 0.00656 ( 1) link_BETA1-4 : angle 0.91747 ( 3) link_BETA1-6 : bond 0.00444 ( 1) link_BETA1-6 : angle 1.23771 ( 3) link_NAG-ASN : bond 0.00620 ( 3) link_NAG-ASN : angle 3.07597 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.36 seconds wall clock time: 33 minutes 14.19 seconds (1994.19 seconds total)