Starting phenix.real_space_refine on Tue Mar 3 19:08:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m42_23662/03_2026/7m42_23662.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m42_23662/03_2026/7m42_23662.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/7m42_23662/03_2026/7m42_23662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2026/7m42_23662.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2026/7m42_23662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m42_23662/03_2026/7m42_23662.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= 0.035 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 31 5.16 5 C 5110 2.51 5 N 1362 2.21 5 O 1612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8115 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1551 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1710 Classifications: {'peptide': 224} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 210} Chain: "E" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1543 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "C" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1572 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 196} Chain: "D" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1700 Classifications: {'peptide': 228} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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 Time building chain proxies: 1.93, per 1000 atoms: 0.24 Number of scatterers: 8115 At special positions: 0 Unit cell: (74.8, 114.75, 148.75, 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 31 16.00 O 1612 8.00 N 1362 7.00 C 5110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 197 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 199 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 155 " - pdb=" SG CYS D 211 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG F 1 " - " ASN E 343 " Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 319.2 milliseconds 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 25 sheets defined 8.7% alpha, 44.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.764A pdb=" N ASP A 84 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 85 " --> pdb=" O ALA A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 85' Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.707A pdb=" N HIS A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.570A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.154A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.024A pdb=" N ASN E 388 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.964A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN E 409 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 410 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 405 through 410' Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 505 Processing helix chain 'C' and resid 127 through 133 Processing helix chain 'C' and resid 187 through 193 removed outlier: 3.619A pdb=" N TRP C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N TRP A 37 " --> pdb=" O MET A 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.409A pdb=" N VAL A 10 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 23 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 122 removed outlier: 6.186A pdb=" N TYR A 176 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 159 removed outlier: 4.378A pdb=" N TRP A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.849A pdb=" N GLU B 10 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 117 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR B 33 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 130 through 134 removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.661A pdb=" N SER B 142 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 145 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 186 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 161 through 164 removed outlier: 4.259A pdb=" N TYR B 204 " --> pdb=" O VAL B 221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.822A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.725A pdb=" N VAL C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 18 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 124 removed outlier: 6.253A pdb=" N TYR C 178 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 159 through 161 removed outlier: 4.497A pdb=" N TRP C 154 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC4, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.920A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 135 through 139 removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 146 through 147 removed outlier: 4.142A pdb=" N SER D 147 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR D 191 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 166 through 169 removed outlier: 4.576A pdb=" N TYR D 209 " --> pdb=" O VAL D 226 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 870 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: 1.30 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: 2583 1.34 - 1.46: 2120 1.46 - 1.58: 3581 1.58 - 1.70: 0 1.70 - 1.83: 38 Bond restraints: 8322 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.71e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.23e+00 bond pdb=" C5 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 1.523 1.537 -0.014 1.27e-02 6.20e+03 1.25e+00 ... (remaining 8317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11155 1.83 - 3.66: 166 3.66 - 5.49: 21 5.49 - 7.32: 4 7.32 - 9.15: 3 Bond angle restraints: 11349 Sorted by residual: angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 109.24 100.09 9.15 1.67e+00 3.59e-01 3.00e+01 angle pdb=" C ASP A 52 " pdb=" N VAL A 53 " pdb=" CA VAL A 53 " ideal model delta sigma weight residual 121.97 128.67 -6.70 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N VAL A 53 " pdb=" CA VAL A 53 " pdb=" C VAL A 53 " ideal model delta sigma weight residual 109.34 116.23 -6.89 2.08e+00 2.31e-01 1.10e+01 angle pdb=" CA LEU C 97 " pdb=" CB LEU C 97 " pdb=" CG LEU C 97 " ideal model delta sigma weight residual 116.30 125.15 -8.85 3.50e+00 8.16e-02 6.39e+00 angle pdb=" CA GLU C 204 " pdb=" CB GLU C 204 " pdb=" CG GLU C 204 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.41e+00 ... (remaining 11344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.96: 4677 21.96 - 43.91: 243 43.91 - 65.87: 33 65.87 - 87.82: 17 87.82 - 109.78: 4 Dihedral angle restraints: 4974 sinusoidal: 1901 harmonic: 3073 Sorted by residual: dihedral pdb=" CB CYS D 155 " pdb=" SG CYS D 155 " pdb=" SG CYS D 211 " pdb=" CB CYS D 211 " ideal model delta sinusoidal sigma weight residual 93.00 44.21 48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 56.19 36.81 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS C 140 " pdb=" SG CYS C 140 " pdb=" SG CYS C 199 " pdb=" CB CYS C 199 " ideal model delta sinusoidal sigma weight residual 93.00 58.27 34.73 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1044 0.052 - 0.103: 176 0.103 - 0.155: 44 0.155 - 0.206: 5 0.206 - 0.258: 2 Chirality restraints: 1271 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LYS D 221 " pdb=" N LYS D 221 " pdb=" C LYS D 221 " pdb=" CB LYS D 221 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1268 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 97 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.69e+00 pdb=" C ALA D 97 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA D 97 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS D 98 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 343 " -0.019 2.00e-02 2.50e+03 1.79e-02 4.02e+00 pdb=" CG ASN E 343 " 0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN E 343 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN E 343 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU D 163 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 164 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 136 2.68 - 3.24: 7148 3.24 - 3.79: 11566 3.79 - 4.35: 15577 4.35 - 4.90: 26834 Nonbonded interactions: 61261 Sorted by model distance: nonbonded pdb=" O ASP A 52 " pdb=" N SER A 54 " model vdw 2.128 3.120 nonbonded pdb=" OG SER A 65 " pdb=" OG1 THR A 76 " model vdw 2.135 3.040 nonbonded pdb=" OG SER D 52 " pdb=" OG SER D 57 " model vdw 2.182 3.040 nonbonded pdb=" OH TYR B 155 " pdb=" OE2 GLU B 158 " model vdw 2.217 3.040 nonbonded pdb=" O HIS A 201 " pdb=" OG SER A 204 " model vdw 2.270 3.040 ... (remaining 61256 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.070 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 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 : 0.002 0.033 8337 Z= 0.104 Angle : 0.571 9.147 11382 Z= 0.300 Chirality : 0.045 0.258 1271 Planarity : 0.004 0.042 1456 Dihedral : 13.897 109.779 2984 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.49 % Favored : 96.42 % Rotamer: Outliers : 1.22 % Allowed : 10.33 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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 are not related in a simple way. whole: -2.65 (0.23), residues: 1060 helix: -3.74 (0.36), residues: 72 sheet: -0.76 (0.23), residues: 438 loop : -2.36 (0.22), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 355 TYR 0.019 0.001 TYR E 351 PHE 0.008 0.001 PHE C 145 TRP 0.006 0.001 TRP B 50 HIS 0.001 0.000 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8322) covalent geometry : angle 0.55731 (11349) SS BOND : bond 0.00221 ( 12) SS BOND : angle 1.93744 ( 24) hydrogen bonds : bond 0.12054 ( 290) hydrogen bonds : angle 6.64306 ( 870) link_BETA1-4 : bond 0.00782 ( 2) link_BETA1-4 : angle 2.33886 ( 6) link_NAG-ASN : bond 0.00325 ( 1) link_NAG-ASN : angle 4.71562 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.285 Fit side-chains REVERT: E 458 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8286 (mttp) REVERT: C 55 ASN cc_start: 0.8319 (m-40) cc_final: 0.8097 (m110) REVERT: C 83 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7361 (tm-30) outliers start: 11 outliers final: 3 residues processed: 136 average time/residue: 0.0678 time to fit residues: 13.3024 Evaluate side-chains 93 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.8980 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 198 GLN E 370 ASN C 16 GLN C 28 ASN C 194 HIS D 170 ASN D 186 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121747 restraints weight = 11335.154| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.76 r_work: 0.3378 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8337 Z= 0.089 Angle : 0.535 11.284 11382 Z= 0.267 Chirality : 0.044 0.173 1271 Planarity : 0.004 0.042 1456 Dihedral : 6.025 60.128 1216 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.60 % Rotamer: Outliers : 2.67 % Allowed : 13.89 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % 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 are not related in a simple way. whole: -1.82 (0.24), residues: 1060 helix: -3.05 (0.43), residues: 74 sheet: -0.17 (0.24), residues: 441 loop : -1.85 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 16 TYR 0.024 0.001 TYR C 93 PHE 0.011 0.001 PHE E 377 TRP 0.007 0.001 TRP B 50 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 8322) covalent geometry : angle 0.52908 (11349) SS BOND : bond 0.00278 ( 12) SS BOND : angle 0.78337 ( 24) hydrogen bonds : bond 0.02737 ( 290) hydrogen bonds : angle 5.16717 ( 870) link_BETA1-4 : bond 0.00650 ( 2) link_BETA1-4 : angle 2.93976 ( 6) link_NAG-ASN : bond 0.00418 ( 1) link_NAG-ASN : angle 2.26612 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.259 Fit side-chains REVERT: E 335 LEU cc_start: 0.5493 (OUTLIER) cc_final: 0.5125 (tt) REVERT: E 354 ASN cc_start: 0.8688 (t0) cc_final: 0.8467 (t0) REVERT: E 458 LYS cc_start: 0.9014 (mtmt) cc_final: 0.8491 (mttp) REVERT: C 83 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 190 GLN cc_start: 0.5925 (mt0) cc_final: 0.5420 (mp10) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 0.0685 time to fit residues: 11.5222 Evaluate side-chains 100 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 HIS E 493 GLN C 6 GLN C 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.165483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118568 restraints weight = 11103.733| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.65 r_work: 0.3332 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8337 Z= 0.103 Angle : 0.527 9.580 11382 Z= 0.263 Chirality : 0.043 0.179 1271 Planarity : 0.004 0.043 1456 Dihedral : 4.633 36.362 1214 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.13 % Rotamer: Outliers : 4.00 % Allowed : 15.00 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.39 (0.24), residues: 1060 helix: -2.60 (0.50), residues: 73 sheet: 0.16 (0.24), residues: 440 loop : -1.63 (0.24), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 16 TYR 0.016 0.001 TYR C 93 PHE 0.007 0.001 PHE A 93 TRP 0.009 0.001 TRP B 50 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8322) covalent geometry : angle 0.52132 (11349) SS BOND : bond 0.00382 ( 12) SS BOND : angle 1.03644 ( 24) hydrogen bonds : bond 0.02728 ( 290) hydrogen bonds : angle 4.95476 ( 870) link_BETA1-4 : bond 0.00929 ( 2) link_BETA1-4 : angle 2.51429 ( 6) link_NAG-ASN : bond 0.00450 ( 1) link_NAG-ASN : angle 1.67786 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.209 Fit side-chains REVERT: E 335 LEU cc_start: 0.5360 (OUTLIER) cc_final: 0.5011 (tt) REVERT: E 354 ASN cc_start: 0.8769 (t0) cc_final: 0.8515 (t0) REVERT: E 420 ASP cc_start: 0.8236 (m-30) cc_final: 0.7993 (m-30) REVERT: E 458 LYS cc_start: 0.9011 (mtmt) cc_final: 0.8441 (mttp) REVERT: C 83 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 190 GLN cc_start: 0.5889 (mt0) cc_final: 0.5378 (mp10) REVERT: D 43 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7474 (mmtm) outliers start: 36 outliers final: 23 residues processed: 122 average time/residue: 0.0639 time to fit residues: 11.5960 Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 4 optimal weight: 0.0770 chunk 101 optimal weight: 0.3980 chunk 102 optimal weight: 5.9990 chunk 103 optimal weight: 30.0000 chunk 100 optimal weight: 30.0000 chunk 52 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.165638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.117382 restraints weight = 11532.527| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.74 r_work: 0.3327 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8337 Z= 0.094 Angle : 0.538 12.595 11382 Z= 0.262 Chirality : 0.043 0.173 1271 Planarity : 0.004 0.044 1456 Dihedral : 4.184 38.627 1214 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.44 % Allowed : 16.78 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.16 (0.25), residues: 1060 helix: -2.55 (0.51), residues: 69 sheet: 0.28 (0.24), residues: 442 loop : -1.43 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 16 TYR 0.011 0.001 TYR D 95 PHE 0.031 0.001 PHE A 143 TRP 0.010 0.001 TRP B 50 HIS 0.002 0.000 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 8322) covalent geometry : angle 0.53461 (11349) SS BOND : bond 0.00290 ( 12) SS BOND : angle 0.78322 ( 24) hydrogen bonds : bond 0.02575 ( 290) hydrogen bonds : angle 4.81473 ( 870) link_BETA1-4 : bond 0.00795 ( 2) link_BETA1-4 : angle 2.27927 ( 6) link_NAG-ASN : bond 0.00402 ( 1) link_NAG-ASN : angle 1.44651 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.215 Fit side-chains REVERT: A 127 GLU cc_start: 0.6741 (mt-10) cc_final: 0.6240 (mp0) REVERT: E 335 LEU cc_start: 0.5331 (OUTLIER) cc_final: 0.4990 (tt) REVERT: E 354 ASN cc_start: 0.8799 (t0) cc_final: 0.8546 (t0) REVERT: E 420 ASP cc_start: 0.8329 (m-30) cc_final: 0.8063 (m-30) REVERT: E 458 LYS cc_start: 0.9004 (mtmt) cc_final: 0.8439 (mttp) REVERT: C 83 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7475 (tm-30) REVERT: C 190 GLN cc_start: 0.5874 (mt0) cc_final: 0.5361 (mp10) REVERT: D 43 LYS cc_start: 0.7820 (mmmm) cc_final: 0.7464 (mmtm) outliers start: 31 outliers final: 24 residues processed: 116 average time/residue: 0.0625 time to fit residues: 10.7407 Evaluate side-chains 113 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 41 HIS E 394 ASN C 6 GLN D 212 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110287 restraints weight = 11535.541| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.20 r_work: 0.3168 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.082 8337 Z= 0.325 Angle : 0.718 10.126 11382 Z= 0.369 Chirality : 0.049 0.203 1271 Planarity : 0.005 0.046 1456 Dihedral : 5.350 43.582 1214 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.26 % Favored : 92.64 % Rotamer: Outliers : 4.44 % Allowed : 18.11 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.51 (0.25), residues: 1060 helix: -2.58 (0.52), residues: 62 sheet: 0.08 (0.25), residues: 442 loop : -1.76 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 72 TYR 0.022 0.002 TYR C 101 PHE 0.019 0.003 PHE D 27 TRP 0.023 0.002 TRP D 53 HIS 0.006 0.002 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00768 ( 8322) covalent geometry : angle 0.71433 (11349) SS BOND : bond 0.00594 ( 12) SS BOND : angle 1.43250 ( 24) hydrogen bonds : bond 0.03900 ( 290) hydrogen bonds : angle 5.66819 ( 870) link_BETA1-4 : bond 0.00793 ( 2) link_BETA1-4 : angle 1.74803 ( 6) link_NAG-ASN : bond 0.00220 ( 1) link_NAG-ASN : angle 1.79340 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.192 Fit side-chains REVERT: A 188 GLN cc_start: 0.7647 (mm-40) cc_final: 0.6621 (tp-100) REVERT: E 335 LEU cc_start: 0.5332 (OUTLIER) cc_final: 0.4996 (tt) REVERT: E 354 ASN cc_start: 0.8923 (t0) cc_final: 0.8696 (t0) REVERT: E 420 ASP cc_start: 0.8492 (m-30) cc_final: 0.8115 (m-30) REVERT: E 458 LYS cc_start: 0.8998 (mtmt) cc_final: 0.8479 (mttp) REVERT: C 83 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7565 (tm-30) REVERT: C 93 TYR cc_start: 0.9126 (t80) cc_final: 0.8687 (t80) REVERT: D 43 LYS cc_start: 0.7612 (mmmm) cc_final: 0.7171 (mmtm) REVERT: D 65 LYS cc_start: 0.8628 (tptt) cc_final: 0.8392 (tttm) REVERT: D 76 LYS cc_start: 0.7969 (mptt) cc_final: 0.7685 (mmtp) outliers start: 40 outliers final: 33 residues processed: 128 average time/residue: 0.0718 time to fit residues: 13.1983 Evaluate side-chains 120 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.110190 restraints weight = 11182.593| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.63 r_work: 0.3220 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8337 Z= 0.170 Angle : 0.608 10.471 11382 Z= 0.307 Chirality : 0.045 0.204 1271 Planarity : 0.004 0.046 1456 Dihedral : 5.051 46.577 1214 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 3.89 % Allowed : 20.11 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.40 (0.25), residues: 1060 helix: -2.65 (0.50), residues: 69 sheet: 0.17 (0.25), residues: 446 loop : -1.66 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 72 TYR 0.027 0.002 TYR D 160 PHE 0.023 0.002 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8322) covalent geometry : angle 0.60472 (11349) SS BOND : bond 0.00437 ( 12) SS BOND : angle 1.05159 ( 24) hydrogen bonds : bond 0.03142 ( 290) hydrogen bonds : angle 5.40347 ( 870) link_BETA1-4 : bond 0.00679 ( 2) link_BETA1-4 : angle 1.66663 ( 6) link_NAG-ASN : bond 0.00141 ( 1) link_NAG-ASN : angle 1.69318 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.283 Fit side-chains REVERT: A 16 GLN cc_start: 0.7366 (mp10) cc_final: 0.6925 (mp10) REVERT: A 49 MET cc_start: 0.8890 (tpp) cc_final: 0.8515 (mmt) REVERT: A 188 GLN cc_start: 0.7687 (mm-40) cc_final: 0.6719 (tp-100) REVERT: E 335 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5117 (tt) REVERT: E 354 ASN cc_start: 0.8875 (t0) cc_final: 0.8660 (t0) REVERT: E 458 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8517 (mttp) REVERT: C 83 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7555 (tm-30) REVERT: C 93 TYR cc_start: 0.9072 (t80) cc_final: 0.8647 (t80) REVERT: C 97 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8806 (pp) REVERT: D 43 LYS cc_start: 0.7688 (mmmm) cc_final: 0.7271 (mmtm) REVERT: D 65 LYS cc_start: 0.8568 (tptt) cc_final: 0.8307 (tttm) REVERT: D 76 LYS cc_start: 0.7956 (mptt) cc_final: 0.7555 (mmtp) outliers start: 35 outliers final: 30 residues processed: 111 average time/residue: 0.0710 time to fit residues: 11.5519 Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 51 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.110766 restraints weight = 11361.584| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.68 r_work: 0.3237 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8337 Z= 0.135 Angle : 0.580 10.055 11382 Z= 0.292 Chirality : 0.044 0.205 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.879 44.916 1214 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.96 % Rotamer: Outliers : 3.56 % Allowed : 21.11 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.19 (0.25), residues: 1060 helix: -2.63 (0.49), residues: 75 sheet: 0.32 (0.25), residues: 441 loop : -1.48 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.030 0.001 TYR D 160 PHE 0.026 0.002 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 8322) covalent geometry : angle 0.57781 (11349) SS BOND : bond 0.00404 ( 12) SS BOND : angle 0.95709 ( 24) hydrogen bonds : bond 0.02911 ( 290) hydrogen bonds : angle 5.25400 ( 870) link_BETA1-4 : bond 0.00661 ( 2) link_BETA1-4 : angle 1.57030 ( 6) link_NAG-ASN : bond 0.00186 ( 1) link_NAG-ASN : angle 1.63894 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.188 Fit side-chains REVERT: A 16 GLN cc_start: 0.7418 (mp10) cc_final: 0.6958 (mp10) REVERT: A 49 MET cc_start: 0.8826 (tpp) cc_final: 0.8493 (mmt) REVERT: A 188 GLN cc_start: 0.7649 (mm-40) cc_final: 0.6692 (tp-100) REVERT: E 335 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.5046 (tt) REVERT: E 354 ASN cc_start: 0.8878 (t0) cc_final: 0.8664 (t0) REVERT: E 458 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8499 (mttp) REVERT: C 83 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7573 (tm-30) REVERT: C 93 TYR cc_start: 0.9032 (t80) cc_final: 0.8613 (t80) REVERT: D 43 LYS cc_start: 0.7656 (mmmm) cc_final: 0.7234 (mmtm) REVERT: D 65 LYS cc_start: 0.8483 (tptt) cc_final: 0.8201 (tttm) REVERT: D 76 LYS cc_start: 0.7955 (mptt) cc_final: 0.7569 (mmtp) outliers start: 32 outliers final: 28 residues processed: 109 average time/residue: 0.0672 time to fit residues: 10.7449 Evaluate side-chains 110 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.158114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109975 restraints weight = 11320.350| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.65 r_work: 0.3226 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8337 Z= 0.155 Angle : 0.594 10.606 11382 Z= 0.298 Chirality : 0.045 0.209 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.924 44.598 1214 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 3.89 % Allowed : 20.78 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.13 (0.25), residues: 1060 helix: -2.55 (0.48), residues: 75 sheet: 0.34 (0.25), residues: 445 loop : -1.44 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.028 0.001 TYR D 160 PHE 0.022 0.002 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8322) covalent geometry : angle 0.59123 (11349) SS BOND : bond 0.00399 ( 12) SS BOND : angle 0.98953 ( 24) hydrogen bonds : bond 0.02994 ( 290) hydrogen bonds : angle 5.25984 ( 870) link_BETA1-4 : bond 0.00645 ( 2) link_BETA1-4 : angle 1.50135 ( 6) link_NAG-ASN : bond 0.00221 ( 1) link_NAG-ASN : angle 1.65179 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.215 Fit side-chains REVERT: A 16 GLN cc_start: 0.7434 (mp10) cc_final: 0.6954 (mp10) REVERT: A 49 MET cc_start: 0.8845 (tpp) cc_final: 0.8270 (mmt) REVERT: A 188 GLN cc_start: 0.7675 (mm-40) cc_final: 0.6714 (tp-100) REVERT: E 335 LEU cc_start: 0.5381 (OUTLIER) cc_final: 0.5088 (tt) REVERT: E 354 ASN cc_start: 0.8899 (t0) cc_final: 0.8682 (t0) REVERT: E 406 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: E 458 LYS cc_start: 0.9041 (mtmt) cc_final: 0.8517 (mttp) REVERT: C 83 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7599 (tm-30) REVERT: C 93 TYR cc_start: 0.9023 (t80) cc_final: 0.8608 (t80) REVERT: D 43 LYS cc_start: 0.7668 (mmmm) cc_final: 0.7253 (mmtm) REVERT: D 65 LYS cc_start: 0.8537 (tptt) cc_final: 0.8298 (tttm) REVERT: D 76 LYS cc_start: 0.7952 (mptt) cc_final: 0.7578 (mmtp) outliers start: 35 outliers final: 32 residues processed: 109 average time/residue: 0.0727 time to fit residues: 11.3721 Evaluate side-chains 113 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 97 optimal weight: 40.0000 chunk 14 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110066 restraints weight = 11383.073| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.68 r_work: 0.3230 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8337 Z= 0.148 Angle : 0.589 12.036 11382 Z= 0.295 Chirality : 0.045 0.213 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.905 44.485 1214 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.66 % Favored : 94.25 % Rotamer: Outliers : 4.11 % Allowed : 20.56 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -1.09 (0.25), residues: 1060 helix: -2.44 (0.51), residues: 69 sheet: 0.34 (0.25), residues: 446 loop : -1.42 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.028 0.001 TYR D 160 PHE 0.024 0.002 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8322) covalent geometry : angle 0.58630 (11349) SS BOND : bond 0.00419 ( 12) SS BOND : angle 0.99180 ( 24) hydrogen bonds : bond 0.02945 ( 290) hydrogen bonds : angle 5.24258 ( 870) link_BETA1-4 : bond 0.00591 ( 2) link_BETA1-4 : angle 1.45393 ( 6) link_NAG-ASN : bond 0.00202 ( 1) link_NAG-ASN : angle 1.67557 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 86 time to evaluate : 0.282 Fit side-chains REVERT: A 16 GLN cc_start: 0.7469 (mp10) cc_final: 0.6983 (mp10) REVERT: A 49 MET cc_start: 0.8843 (tpp) cc_final: 0.8282 (mmt) REVERT: A 188 GLN cc_start: 0.7658 (mm-40) cc_final: 0.6711 (tp-100) REVERT: E 335 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.5031 (tt) REVERT: E 354 ASN cc_start: 0.8891 (t0) cc_final: 0.8671 (t0) REVERT: E 406 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: E 458 LYS cc_start: 0.9043 (mtmt) cc_final: 0.8505 (mttp) REVERT: C 83 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7611 (tm-30) REVERT: C 93 TYR cc_start: 0.9028 (t80) cc_final: 0.8611 (t80) REVERT: D 43 LYS cc_start: 0.7657 (mmmm) cc_final: 0.7238 (mmtm) REVERT: D 65 LYS cc_start: 0.8546 (tptt) cc_final: 0.8308 (tttm) REVERT: D 76 LYS cc_start: 0.7953 (mptt) cc_final: 0.7583 (mmtp) outliers start: 37 outliers final: 34 residues processed: 113 average time/residue: 0.0666 time to fit residues: 11.0098 Evaluate side-chains 120 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 41 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.159279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112059 restraints weight = 11175.891| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.65 r_work: 0.3248 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8337 Z= 0.120 Angle : 0.573 11.888 11382 Z= 0.286 Chirality : 0.044 0.209 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.766 43.665 1214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.67 % Allowed : 21.22 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.97 (0.25), residues: 1060 helix: -2.41 (0.50), residues: 75 sheet: 0.43 (0.25), residues: 445 loop : -1.31 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 72 TYR 0.029 0.001 TYR D 160 PHE 0.025 0.001 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.003 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8322) covalent geometry : angle 0.57048 (11349) SS BOND : bond 0.00367 ( 12) SS BOND : angle 0.85923 ( 24) hydrogen bonds : bond 0.02777 ( 290) hydrogen bonds : angle 5.12469 ( 870) link_BETA1-4 : bond 0.00626 ( 2) link_BETA1-4 : angle 1.46279 ( 6) link_NAG-ASN : bond 0.00238 ( 1) link_NAG-ASN : angle 1.67204 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2120 Ramachandran restraints generated. 1060 Oldfield, 0 Emsley, 1060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.177 Fit side-chains REVERT: A 16 GLN cc_start: 0.7406 (mp10) cc_final: 0.6907 (mp10) REVERT: A 49 MET cc_start: 0.8802 (tpp) cc_final: 0.8457 (mmt) REVERT: A 188 GLN cc_start: 0.7681 (mm-40) cc_final: 0.6782 (tp-100) REVERT: E 335 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4994 (tt) REVERT: E 354 ASN cc_start: 0.8877 (t0) cc_final: 0.8643 (t0) REVERT: E 458 LYS cc_start: 0.9042 (mtmt) cc_final: 0.8408 (mttp) REVERT: C 83 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 93 TYR cc_start: 0.8994 (t80) cc_final: 0.8629 (t80) REVERT: D 43 LYS cc_start: 0.7638 (mmmm) cc_final: 0.7239 (mmtm) REVERT: D 65 LYS cc_start: 0.8421 (tptt) cc_final: 0.8196 (tttm) REVERT: D 76 LYS cc_start: 0.7907 (mptt) cc_final: 0.7538 (mmtp) outliers start: 33 outliers final: 30 residues processed: 108 average time/residue: 0.0711 time to fit residues: 11.1579 Evaluate side-chains 115 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASP Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 478 THR Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain C residue 16 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 216 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.157931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110735 restraints weight = 11238.683| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.63 r_work: 0.3231 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8337 Z= 0.151 Angle : 0.590 12.537 11382 Z= 0.296 Chirality : 0.045 0.212 1271 Planarity : 0.004 0.046 1456 Dihedral : 4.879 43.545 1214 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.32 % Favored : 93.58 % Rotamer: Outliers : 3.78 % Allowed : 20.89 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 are not related in a simple way. whole: -0.97 (0.25), residues: 1060 helix: -2.33 (0.53), residues: 69 sheet: 0.42 (0.25), residues: 446 loop : -1.35 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 72 TYR 0.028 0.001 TYR D 160 PHE 0.022 0.002 PHE A 143 TRP 0.014 0.001 TRP B 50 HIS 0.004 0.001 HIS D 215 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8322) covalent geometry : angle 0.58805 (11349) SS BOND : bond 0.00416 ( 12) SS BOND : angle 0.97375 ( 24) hydrogen bonds : bond 0.02939 ( 290) hydrogen bonds : angle 5.18223 ( 870) link_BETA1-4 : bond 0.00586 ( 2) link_BETA1-4 : angle 1.42826 ( 6) link_NAG-ASN : bond 0.00223 ( 1) link_NAG-ASN : angle 1.69661 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.11 seconds wall clock time: 42 minutes 2.59 seconds (2522.59 seconds total)